diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index d6038ff951..9a8675a013 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -25,18 +25,32 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        java_version: [11, 17, 22]
+        java_version: [17, 23]
 
     steps:
-      - name: Environment
-        run: env | sort
-
       - name: Checkout
         uses: actions/checkout@v4
         with:
           fetch-depth: 1
           submodules: true
 
+      - name: Get the commit message
+        id: get_commit_message
+        run: |
+            if [ "${{ github.event_name }}" = "pull_request" ]; then
+                echo "GitHub event=pull_request"
+                COMMIT_SHA=${{ github.event.pull_request.head.sha }}
+                COMMIT_MESSAGE=$(curl -s \
+                  -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
+                  https://api.github.com/repos/${{ github.repository }}/commits/$COMMIT_SHA | jq -r '.commit.message')
+                echo "Commit message=$COMMIT_MESSAGE" | head -n 1
+                echo "commit_message=$COMMIT_MESSAGE" | head -n 1 >> $GITHUB_OUTPUT
+            else
+               echo "GitHub event=${{ github.event_name }}"
+               echo "Commit message=${{ github.event.head_commit.message }}" | head -n 1
+               echo "commit_message=${{ github.event.head_commit.message }}" | head -n 1 >> $GITHUB_OUTPUT
+            fi 
+
       - name: Get changed files
         id: changed-files
         uses: tj-actions/changed-files@v43
@@ -76,6 +90,7 @@ jobs:
       - name: Test
         if: steps.changed-files.outputs.any_changed == 'true'
         run: |
+            env | sort
             # configure test env
             if [[ "$GOOGLE_SECRET" ]]; then
             echo $GOOGLE_SECRET | base64 -d > $PWD/google_credentials.json
@@ -106,16 +121,17 @@ jobs:
 
     outputs:
       any_changed: ${{ steps.changed-files.outputs.any_changed }}
+      commit_message: ${{ steps.get_commit_message.outputs.commit_message }}
 
   test:
-    if: ${{ !contains(github.event.head_commit.message, '[ci fast]') && needs.build.outputs.any_changed == 'true' }}
+    if: ${{ !contains(needs.build.outputs.commit_message, '[ci fast]') && needs.build.outputs.any_changed == 'true' }}
     needs: build
     runs-on: ubuntu-latest
     timeout-minutes: 90
     strategy:
       fail-fast: false
       matrix:
-        java_version: [11, 21]
+        java_version: [17, 23]
         test_mode: ["test_integration", "test_docs", "test_aws", "test_azure", "test_google", "test_wave"]
     steps:
       - name: Checkout
@@ -142,6 +158,12 @@ jobs:
 
       - name: Run tests
         run: |
+          env | sort
+          # configure test env
+          if [[ "$GOOGLE_SECRET" ]]; then
+          echo $GOOGLE_SECRET | base64 -d > $PWD/google_credentials.json
+          export GOOGLE_APPLICATION_CREDENTIALS=$PWD/google_credentials.json
+          fi
           cat $HOME/.nextflow/scm
           make clean assemble install
           bash test-ci.sh
@@ -173,5 +195,51 @@ jobs:
         with:
           name: report-${{ matrix.test_mode }}-jdk-${{ matrix.java_version }}
           path: |
-            validation/**
+            validation/**/*
+            validation/**/.*
             integration-tests.tar
+
+  test-e2e:
+      if: ${{ contains(needs.build.outputs.commit_message,'[e2e stage]') || contains(needs.build.outputs.commit_message,'[e2e prod]') }}
+      needs: build
+      runs-on: ubuntu-latest
+      timeout-minutes: 10
+      permissions:
+          actions: write  # Allow writing to actions
+          contents: write # Allow writing to repository contents
+      steps:
+          - name: Checkout
+            uses: actions/checkout@v4
+            with:
+                fetch-depth: 1
+                submodules: true
+                
+          - name: Setup Java 17
+            uses: actions/setup-java@v4
+            with:
+                java-version: 17
+                distribution: 'temurin'
+                architecture: x64
+                cache: gradle
+
+          - name: Setup env
+            run: |
+                wget -q -O wave https://github.com/seqeralabs/wave-cli/releases/download/v1.4.1/wave-1.4.1-linux-x86_64
+                chmod +x wave
+                mv wave /usr/local/bin/
+                echo "COMMIT_MESSAGE=\"${{ needs.build.outputs.commit_message }}\"" >> $GITHUB_ENV
+
+          - name : Docker Login to Seqera public CR
+            uses : docker/login-action@v3
+            with :
+                registry : "public.cr.seqera.io"
+                username : "public-cr-admin"
+                password : ${{ secrets.SEQERA_PUBLIC_CR_PASSWORD }}
+
+          - name: Launch tests
+            run: |
+                cd test-e2e
+                bash run.sh
+            env:
+                GITHUB_TOKEN: ${{ secrets.AUTOMATION_GITHUB_TOKEN }}
+                GRADLE_OPTS: '-Dorg.gradle.daemon=false'
diff --git a/.github/workflows/generate-send-dependencies.yml b/.github/workflows/generate-send-dependencies.yml
new file mode 100644
index 0000000000..639b28a7ad
--- /dev/null
+++ b/.github/workflows/generate-send-dependencies.yml
@@ -0,0 +1,27 @@
+name: Generate and submit dependency graph for nextflow
+on:
+    push:
+      branches: ['master']
+
+permissions:
+  contents: write
+
+jobs:
+  dependency-submission:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        components: ["nextflow", "plugins:nf-google", "plugins:nf-amazon", "plugins:nf-azure", "plugins:nf-cloudcache", "plugins:nf-codecommit", "plugins:nf-console", "plugins:nf-tower", "plugins:nf-wave"]
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-java@v4
+      with:
+        distribution: temurin
+        java-version: 21
+
+    - name: Generate and submit dependency graph for nextflow
+      uses: gradle/actions/dependency-submission@v4
+      with:
+        dependency-resolution-task: ":${{ matrix.components }}:dependencies"
+        additional-arguments: "--configuration runtimeClasspath"
+        dependency-graph: generate-and-submit
diff --git a/.github/workflows/seqeradocs-changelog.yml b/.github/workflows/seqeradocs-changelog.yml
new file mode 100644
index 0000000000..f41058fe71
--- /dev/null
+++ b/.github/workflows/seqeradocs-changelog.yml
@@ -0,0 +1,62 @@
+name: Push release change log to Seqera Docs
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+    inputs:
+      release_name:
+        description: "Release version (e.g. 1.0.0)"
+        required: true
+      release_body:
+        description: "Release changelog content"
+        required: true
+
+jobs:
+  update-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Clone seqeralabs/docs
+        run: |
+          git clone https://github.com/seqeralabs/docs.git seqeralabs-docs
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Create changelog file
+        run: |
+          mkdir -p seqeralabs-docs/changelog/nextflow
+          cat << EOF > seqeralabs-docs/changelog/nextflow/${{ github.event.release.name || inputs.release_name }}.mdx
+          ---
+          title: Nextflow ${{ github.event.release.name || inputs.release_name }}
+          date: $(date +%Y-%m-%d)
+          tags: [nextflow]
+          ---
+
+          ${{ github.event.release.body || inputs.release_body }}
+          EOF
+
+      - uses: actions/create-github-app-token@v1
+        id: generate-token
+        with:
+          app-id: ${{ secrets.DOCS_BOT_APP_ID }}
+          private-key: ${{ secrets.DOCS_BOT_APP_PRIVATE_KEY }}
+          owner: seqeralabs
+          repositories: docs
+
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@v7
+        with:
+          token: ${{ steps.generate-token.outputs.token }}
+          branch-token: ${{ steps.generate-token.outputs.token }}
+          path: seqeralabs-docs
+          commit-message: "Changelog: Nextflow ${{ github.event.release.name || inputs.release_name }}"
+          title: "Changelog: Nextflow ${{ github.event.release.name || inputs.release_name }}"
+          body: |
+            This PR adds the changelog for Nextflow ${{ github.event.release.name || inputs.release_name }} to the Seqera documentation.
+
+            This is an automated PR created from the Nextflow repository.
+          branch: changelog-nextflow-${{ github.event.release.name || inputs.release_name }}
+          base: master
+          delete-branch: true
diff --git a/VERSION b/VERSION
index d4c0237907..2b70d664e4 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-24.07.0-edge
+24.11.0-edge
diff --git a/build.gradle b/build.gradle
index a0c72f271a..33c367f0e0 100644
--- a/build.gradle
+++ b/build.gradle
@@ -15,7 +15,7 @@
  */
 
 plugins {
-    id "io.codearte.nexus-staging" version "0.21.2"
+    id "io.codearte.nexus-staging" version "0.30.0"
     id 'java'
     id 'idea'
 }
@@ -73,12 +73,12 @@ allprojects {
     }
 
     compileJava {
-        options.release.set(11)
+        options.release.set(17)
     }
 
     tasks.withType(GroovyCompile) {
-        sourceCompatibility = '11'
-        targetCompatibility = '11'
+        sourceCompatibility = '17'
+        targetCompatibility = '17'
     }
 
     idea {
@@ -109,8 +109,8 @@ allprojects {
 
         // Documentation required libraries
         groovyDoc 'org.fusesource.jansi:jansi:2.4.0'
-        groovyDoc "org.apache.groovy:groovy-groovydoc:4.0.22"
-        groovyDoc "org.apache.groovy:groovy-ant:4.0.22"
+        groovyDoc "org.apache.groovy:groovy-groovydoc:4.0.24"
+        groovyDoc "org.apache.groovy:groovy-ant:4.0.24"
     }
 
     test {
@@ -147,7 +147,6 @@ allprojects {
     // Required to run tests on Java 9 and higher in compatibility mode
     tasks.withType(Test) {
         jvmArgs ([
-            '-Dorg.spockframework.mock.ignoreByteBuddy=true',
             '--enable-preview',
             '--add-opens=java.base/java.lang=ALL-UNNAMED',
             '--add-opens=java.base/java.io=ALL-UNNAMED',
diff --git a/buildSrc/build.gradle b/buildSrc/build.gradle
index fa35d4112b..888b0de54a 100644
--- a/buildSrc/build.gradle
+++ b/buildSrc/build.gradle
@@ -11,7 +11,7 @@ version = "1.0.1"
 group = "io.nextflow"
 
 dependencies {
-    implementation ('com.amazonaws:aws-java-sdk-s3:1.12.129')
+    implementation ('com.amazonaws:aws-java-sdk-s3:1.12.777')
     implementation 'com.google.code.gson:gson:2.10.1'
 }
 
diff --git a/changelog.txt b/changelog.txt
index 33b8299300..54fba39ad4 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -1,10 +1,155 @@
 NEXTFLOW CHANGE-LOG
 ===================
+24.11.0-edge - 3 Dec 2024
+- Add GHA to submit dependencies to dependabot (#5440) [80395a6d]
+- Add NotFoundException to retry condition for Google Batch [aa4d19cc]
+- Add Rahel Hirsch to run name generator (#5442) [ff2bc6ae]
+- Add `env()` function (#5506) [fa0e8e0f]
+- Add more scientists to run name generator (#5447) [38d9eda0]
+- Add `singularity.libraryDir` to config page (#5498) [b5e31bb0]
+- Add RepositoryProvider.revision now public property (#5500) [f0a4c526]
+- Deprecate process `shell` block (#5508) [6f527551]
+- Detecting errors in data unstaging (#5345) [3c8e602d]
+- Disable virtual threads on CI tests [ci slip] [69d07dbc]
+- Fix Fargate warning on memory check (#5475) [bdf0ad00]
+- Fix `isContainerReady` when wave is disabled (#5509) [3215afa8]
+- Fix missing wave response (#5547) [ee252173]
+- Fix overlapping conda lock file (#5540) [9248c04d]
+- Fix overlapping conda lock exception (#5489) [eaaeb3de]
+- Fix possible deadlock in dynamic `maxRetry` resolution (#5474) [25bbb621]
+- Fix Wave GCP integration test (#5490) [ad56c89b]
+- Fixing bug when execution with stub and no stub defined (#5473) [f7fd56db]
+- Fix Incorrect CPU value in Azure example (#5549) [fc5e2c2a]
+- Improve docs for using the GPU accelerator directive (#5488) [4b908524]
+- Improve groupTuple docs with scatter/gather example (#5520) [b5c63a9f]
+- Prevent NPE with null AWS Batch response [12fc1d60]
+- Target Java 17 as minimal Java version (#5045) [0140f954]
+- Update 'nexus-staging' plugin to latest version (#5462) [07934513]
+- Update gradle 'shadow' plugin version to 8.3.5 (#5463) [2a5f15f0]
+- Update install docs to reflect change from 'all' to 'dist' (#5496) [c9115659]
+- Update process snippets to comply with strict syntax (#5526) [be1694bf]
+- Update Wave dependencies [09ccd295]
+- Bump aws sdk 1.12.777 (#5458) [8bad0b4b]
+- Bump bouncycastle to jdk18on:1.78.1  (#5467) [cd8c385f]
+- Bump com.azure:azure-identity from 1.11.3 to 1.12.2 (#5449) [cb70f1df]
+- Bump commons-io:2.15.1 [767e4a0a]
+- Bump groovy 4.0.24 [dd71ad31]
+- Bump netty-common to version 4.1.115.Final [d1bbd3d0]
+- Bump nf-amazon@2.10.0 [2b653b07]
+- Bump nf-azure@1.11.0 [6af7198d]
+- Bump nf-google@1.16.0 [9494f970]
+- Bump nf-google@1.8.0 [7e2c8d82]
+- Bump protobuf-java:3.25.5 to nf-google [488b7906]
+
+24.10.2 - 27 Nov 2024
+- Prevent NPE with null AWS Batch response [3d491934]
+- Fix overlapping conda lock file (#5540) [df66deaa]
+- Fix missing wave response (#5547) [eb85cda8]
+- Bump nf-wave@1.7.4 [93d09404]
+- Bump nf-amazon@2.9.2 [469a35dd]
+
+24.10.1 - 18 Nov 2024
+- Fix overlapping file lock exception (#5489) [a2566d54]
+- Fix isContainerReady when wave is disabled (#5509) [c69e3711]
+- Bump nf-wave@1.7.3 [e7709a0f]
+- Bump nf-azure@1.10.2 [54496ac4]
+- Bump nf-amazon@2.9.1 [fa227933]
+- Bump netty-common to version 4.1.115.Final [90623c1e]
+
+24.10.0 - 27 Oct 2024
+- Add `manifest.contributors` config option (#5322) [cf0f9690]
+- Add wave mirror and scan config [92e69776]
+- Add wave mirror vs module bundles conflicst warning [b37a8a5b]
+- Add Workflow output definition (second preview) (#5185) [ea128463]
+- Demote azure batch task status log level to trace (#5416) [d6c684bb]
+- Document formal script syntax (#5336) [a48ac589]
+- Add Expose trace record meta info in the task context (#5402) [ffdd3819]
+- Fix NextflowMeta compilation error [500f49c0]
+- Fix XFileSystem serialization issue (#5411) [711864fd]
+- Fix closure rendering in yaml and json config (#5408) [d3a85ceb]
+- Fix failing docs snippet (#5430) [a818f4b8]
+- Fix http files stream  (#5405) [e2e stage] [718dcbe6]
+- Fix nf-tower plugin to upload logs when early failures  (#5434) [4222442a]
+- Fix support for micromamba (#4302) [12431302]
+- Harmonise documentation for hybrid cloud execution (#5362) [a69407d2]
+- Prevent NPE when containerInfo is null [368a266a]
+- Remove invalid equals char (#5414) [7f39e6ed]
+- Bump nf-azure@1.10.1 [f67e157a]
+- Bump nf-tower@1.9.3 [7a572a12]
+- Bump nf-wave@1.7.2 [6524d8dc]
+
+24.09.2-edge - 14 Oct 2024
+- Add Google LS deprecation notice (#5400) [0ee1d9bc]
+- Add hybrid workflow documentation for Azure (#5361) [f81f27de]
+- Add more out formats to config command (#5399) [8acdb6e8]
+- Change to scan.levels to scan.allowedLevels (#5401) [88a1b1b5]
+- Fix inspect concretize option [0ee29a87]
+- Manage moduleBinaries feature flag in the pipeline script (#5348) [dd5fd20f]
+- Bump nf-wave@1.7.1 [94273967]
+- Bump nf-google@1.15.2 [fab01d58]
+
+24.09.1-edge - 13 Oct 2024
+- Add retry policy in Channel.fromSRA factory (#5389) [fb1c8b2e]
+- Add retry policy to Google batch describe task (#5356) [64bb5a92]
+- Add support for Wave  container status API  (#5384) [873703ad] [9ed18a88]
+- Fix Identify default git branch when downloading pipelines (#3593) (#5375) [4f74fc37]
+- Fix issue when retrying with stub (#5359) [324b611f]
+- Fix include aborted in the ProgressRecord total count (#5365) [8eb0c393]
+- Redirect logs to stderr during app bootstrap (#5206) [94918105]
+- Remove unused reportsOpts (#5379) [e794e868]
+- Sunsetting Spack support in Wave [3a54cb3b] [7bbba67b]
+- Bump nf-google@1.15.1 [4204435e]
+- Bump nf-wave@1.7.0 [cdecb3f5]
+
+24.09.0-edge - 2 Oct 2024
+- Add Fusion version pinning info to Fusion config scope (#5294) [be1cac37]
+- Add container tip in the task error report (#5299) [62e26043]
+- Add support for Java 23 (#5329) [6e10c372]
+- Add Platform workflow prefix in AWS Batch job names (#5318) [42dd4ba8]
+- Fix AWS spot attempts with zero value (#5331) [bac2da12]
+- Fix Azure Fusion env misses credentials when no key or SAS provided (#5328) [e11382c8]
+- Fix CI build taking only the commit msg header [9e702c4d]
+- Fix Inconsistency with camelCase and kebab-case config params #4702 (solve #4033) [349f4f6f]
+- Fix XPath default de-serializer issue (#5339) [290f2d07]
+- Fix failOnIgnore causes task monitor to stop submitting tasks (#5293) [d6870335]
+- Fix large mermaid diagrams (#5302) [a46edfa0]
+- Improve Wave build timeout handling (#5304) [05bef7e4]
+- Include additional fields to manifest (#5314) [33fab52d]
+- Remove `mini` from Flux submit command (#5229) [a0f69025]
+- Update container handling with charliecloud (#5300) [8e6068db]
+- Update Documentation structure (#4766) [25e5eba0]
+- Update nextflow install docs (#5198) [7c453815]
+- Bump groovy 4.0.23 (#5303) [fe3e3ac7]
+- Bump nf-wave@1.6.0 [179093dc]
+- Bump nf-azure@1.10.0 [41d37fa8]
+- Bump nf-amazon@2.9.0 [e38980fb]
+
+24.08.0-edge - 4 Sep 2024
+- Add Google Batch warning when for conflicting disk image config (#5279) [96cb57cb]
+- Add support for Google Batch used specified boot images  (#5268) [0aaa6482]
+- Disable AWS spot retry (#5215) [f28fcb25]
+- Disable Google Batch automatic spot retries (#5223) [aad21533]
+- Disable automatic detection of virtual threads (#5270) [b3ba2c2d]
+- Fix  missing .command.env when eval is used and task runs on a cloud env [4a6b54aa]
+- Fix job array syntax for PBS/Torque executor (#5281) [d59f5fae]
+- Fix k8s client status cond is possible null in podState (#5264) [46672415]
+- Fix non-determinist behaviour of join operator with bag array as key (#5189) [e7dc0d69]
+- Fix stage retry on corrupted HTTP downloads  (#5275) [bf0cd326]
+- Support Azure Managed Identities in Fusion configuration logic (#5278) [a0bf8b40]
+- Use public.cr.seqera.io in place of AWS ECR [5a01f277]
+- Wave client logs improvement [5a37e617]
+- Bump amazoncorretto:21-al2023 [59aed581]
+- Bump nf-wave@1.5.1 [97c4e08f]
+- Bump nf-google@1.15.0 [24133f2a]
+- Bump nf-azure@1.9.0 [29f49ba7]
+- Bump nf-amazon@2.8.0 [bbc3adca]
+
 24.07.0-edge - 8 Aug 2024
 - Add runtime error for missing channel factory (#5170) [1f9210ab]
 - Apply k8s.cpuLimits to kuberun driver pod (#5160) [4300adf1]
 - Await build completion for all Wave containers [2b8117e9]
-- Deprecate module addParams() and params() (#5200) [ci fast] [82c97f8c]
+- Deprecate module addParams() and params() (#5200) [82c97f8c]
+- Remove capsule launcher dependencies (#3395) [f15e4246]
 - Fix AWS Cloudwatch access when using custom log group name [30195838]
 - Fix Invalid AWS Fargate CPUs usage error reporting [d9c50e59]
 - Fix Prevent AwS Batch retry the job execution when the container does not exist [4e218f22]
@@ -60,7 +205,7 @@ NEXTFLOW CHANGE-LOG
 - Bump jgit 6.10.0 [4cf6b9f7]
 
 24.04.3 - 9 Jul 2024
-- Add ability to override failOnError setting default via env variable (#5117) [ci fast] [6852429c]
+- Add ability to override failOnError setting default via env variable (#5117) [6852429c]
 - Fix normalization of consecutive slashes in uri path (#5114) [3f366b7e]
 - Fix executions hangs on finalisation exception (#5070) [4c207c23]
 - Bump nf-google@1.13.2-patch1 [55ec5ec5]
diff --git a/docker-scratch/Dockerfile b/docker-scratch/Dockerfile
deleted file mode 100644
index c2919602af..0000000000
--- a/docker-scratch/Dockerfile
+++ /dev/null
@@ -1,11 +0,0 @@
-FROM amazoncorretto:17-al2023
-COPY .nextflow /.nextflow
-COPY nextflow /usr/bin/nextflow
-ENV NXF_HOME=/.nextflow
-RUN nextflow info
-RUN NXF_PLUGINS_DEFAULT=false nextflow plugin install nf-tower,nf-wave,nf-cloudcache,nf-azure,nf-google,nf-amazon,xpack-amzn,xpack-google,nf-cloudcache
-
-#FROM scratch
-#COPY --from=0 /.nextflow /.nextflow
-#COPY --from=0 /usr/bin/nextflow /usr/bin/nextflow
-
diff --git a/docker-scratch/make.sh b/docker-scratch/make.sh
deleted file mode 100644
index 8217e6b44b..0000000000
--- a/docker-scratch/make.sh
+++ /dev/null
@@ -1,58 +0,0 @@
-#
-# Copyright 2013-2024, Seqera Labs
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-#
-
-# cleanup
-rm -rf .nextflow && mkdir .nextflow
-# copy nextflow dependencies
-(cd ..
-./gradlew compile assemble
-BUILD_PACK=1 ./gradlew installScratch publishToMavenLocal -Dmaven.repo.local=${PWD}/docker-scratch/.nextflow/capsule/deps/
-)
-
-# copy nextflow launcher script
-cp ../nextflow . && chmod +x nextflow
-cp ../modules/nextflow/src/main/resources/META-INF/build-info.properties .
-source build-info.properties
-
-if [ -z "$version" ]; then
-    echo "Error: version is empty or missing"; exit 1
-fi
-if [ -z "$build" ]; then
-    echo "Error: build is empty or missing"; exit 1
-fi
-if [ -z "$commitId" ]; then
-    echo "Error: commitId is empty or missing"; exit 1
-fi
-
-
-TAG=${version}-${commitId}
-repository=${repository:-'docker.io/pditommaso/nf-launcher-dev'}
-image=${repository}:${TAG}
-base=${base:-'docker.io/pditommaso/nf-lancher:j17-base'}
-
-docker buildx build \
-  --no-cache \
-  --platform linux/amd64 \
-  --output=type=docker \
-  --progress=plain \
-  --tag ${image} \
-  --build-arg TARGETPLATFORM=linux/amd64 \
-  .
-
-#launcher=$(wave -i ${base} --include ${image} --config-env NXF_HOME=/.nextflow)
-#
-#echo $launcher
diff --git a/docker/Makefile b/docker/Makefile
index 894e568577..e65294f7fe 100644
--- a/docker/Makefile
+++ b/docker/Makefile
@@ -24,14 +24,10 @@ build-arm: dist/docker/arm64
 	docker buildx build --platform linux/arm64 --output=type=docker --progress=plain --tag nextflow/nextflow:${version} --build-arg TARGETPLATFORM=linux/arm64 .
 
 release: build
-	docker tag nextflow/nextflow:${version} nextflow/nextflow:latest
 	docker push nextflow/nextflow:${version}
-	docker push nextflow/nextflow:latest
 	#
-	docker tag nextflow/nextflow:${version} public.ecr.aws/seqera-labs/nextflow:${version}
-	docker tag nextflow/nextflow:${version} public.ecr.aws/seqera-labs/nextflow:latest
-	docker push public.ecr.aws/seqera-labs/nextflow:${version}
-	docker push public.ecr.aws/seqera-labs/nextflow:latest
+	docker tag nextflow/nextflow:${version} public.cr.seqera.io/nextflow/nextflow:${version}
+	docker push public.cr.seqera.io/nextflow/nextflow:${version}
 
 #Static builds can now be found at:
 #
diff --git a/docs/Dockerfile b/docs/Dockerfile
index 967b660bd3..a961249faf 100644
--- a/docs/Dockerfile
+++ b/docs/Dockerfile
@@ -1,6 +1,4 @@
-FROM mambaorg/micromamba:1.3.1
-
-MAINTAINER Ben Sherman <bentshermann@gmail.com>
+FROM mambaorg/micromamba:1.5.8
 
 RUN micromamba install --yes --name base --channel conda-forge \
       make=4.3 \
diff --git a/docs/_static/dag.mmd b/docs/_static/dag.mmd
index 0963e2c106..989a536ae9 100644
--- a/docs/_static/dag.mmd
+++ b/docs/_static/dag.mmd
@@ -1,3 +1,17 @@
+%%{
+    init: {
+        'theme': 'base',
+        'themeVariables': {
+            'primaryColor': '#B6ECE2',
+            'primaryTextColor': '#160F26',
+            'primaryBorderColor': '#065647',
+            'lineColor': '#545555',
+            'clusterBkg': '#BABCBD22',
+            'clusterBorder': '#DDDEDE',
+            'fontFamily': 'arial'
+        }
+    }
+}%%
 flowchart TB
     subgraph " "
     v0["Channel.fromFilePairs"]
diff --git a/docs/_static/report-resource-memory.png b/docs/_static/report-resource-memory.png
deleted file mode 100644
index 9460c5b343..0000000000
Binary files a/docs/_static/report-resource-memory.png and /dev/null differ
diff --git a/docs/_templates/layout.html b/docs/_templates/layout.html
index f928363914..ad62698389 100644
--- a/docs/_templates/layout.html
+++ b/docs/_templates/layout.html
@@ -10,7 +10,7 @@
         <select onchange="window.location = this.value;">
             <option value="/docs/stable/index.html" {% if version_selected == 'stable' %}selected{% endif %}>Stable</option>
             <option value="/docs/edge/index.html" {% if version_selected == 'edge' %}selected{% endif %}>Edge</option>
-            <option value="/docs/latest/index.html" {% if version_selected == 'dev' %}selected{% endif %}>Development</option>
+            <option value="/docs/latest/index.html" {% if version_selected == 'dev' %}selected{% endif %}>Latest</option>
         </select>
         </select>
     </div>
@@ -21,7 +21,7 @@
     <div class="nav-footer-logo">
         <a href="https://seqera.io/" target="_blank" title="Developed by Seqera Labs">
             Nextflow is developed by:<br>
-            <img src="_static/seqera-logo.svg" alt="Seqera Labs">
+            <img src="{{ pathto('_static/seqera-logo.svg', 1) }}" alt="Seqera Labs">
         </a>
     </div>
 {% endblock %}
diff --git a/docs/amazons3.md b/docs/amazons3.md
index 41bcb407fa..6da7ac4b0d 100644
--- a/docs/amazons3.md
+++ b/docs/amazons3.md
@@ -1,6 +1,6 @@
 (amazons3-page)=
 
-# AWS S3 storage
+# Amazon S3
 
 Nextflow includes support for AWS S3 storage. Files stored in an S3 bucket can be accessed transparently in your pipeline script like any other file in the local file system.
 
@@ -16,11 +16,11 @@ s3://my-bucket/data/sequences.fa
 
 The usual file operations can be applied to a path handle with the above notation. For example, the content of an S3 file can be printed as follows:
 
-```groovy
+```nextflow
 println file('s3://my-bucket/data/sequences.fa').text
 ```
 
-See the {ref}`script-file-io` section to learn more about available file operations.
+See {ref}`working-with-files` and the {ref}`stdlib-types-path` reference to learn more about available file operations.
 
 ## Security credentials
 
diff --git a/docs/aws.md b/docs/aws.md
index abecc989ed..3de628e3cc 100644
--- a/docs/aws.md
+++ b/docs/aws.md
@@ -1,6 +1,6 @@
 (aws-page)=
 
-# AWS Cloud
+# Amazon Web Services
 
 :::{tip}
 This page describes how to manually set up and use Nextflow with AWS Cloud.
@@ -46,53 +46,54 @@ Minimal permissions policies to be attached to the AWS account used by Nextflow
 - To use AWS Batch:
 
   ```json
-  "batch:DescribeJobQueues"
   "batch:CancelJob"
-  "batch:SubmitJob"
-  "batch:ListJobs"
   "batch:DescribeComputeEnvironments"
-  "batch:TerminateJob"
+  "batch:DescribeJobDefinitions"
+  "batch:DescribeJobQueues"
   "batch:DescribeJobs"
+  "batch:ListJobs"
   "batch:RegisterJobDefinition"
-  "batch:DescribeJobDefinitions"
+  "batch:SubmitJob"
+  "batch:TagResource"
+  "batch:TerminateJob"
   ```
 
 - To view [EC2](https://aws.amazon.com/ec2/) instances:
 
   ```json
-  "ecs:DescribeTasks"
+  "ec2:DescribeInstanceAttribute"
   "ec2:DescribeInstances"
+  "ec2:DescribeInstanceStatus"
   "ec2:DescribeInstanceTypes"
-  "ec2:DescribeInstanceAttribute"
   "ecs:DescribeContainerInstances"
-  "ec2:DescribeInstanceStatus"
+  "ecs:DescribeTasks"
   ```
 
 - To pull container images from [ECR](https://aws.amazon.com/ecr/) repositories:
 
   ```json
-  "ecr:GetAuthorizationToken"
   "ecr:BatchCheckLayerAvailability"
-  "ecr:GetDownloadUrlForLayer"
-  "ecr:GetRepositoryPolicy"
-  "ecr:DescribeRepositories"
-  "ecr:ListImages"
-  "ecr:DescribeImages"
   "ecr:BatchGetImage"
+  "ecr:DescribeImages"
+  "ecr:DescribeImageScanFindings"
+  "ecr:DescribeRepositories"
+  "ecr:GetAuthorizationToken"
+  "ecr:GetDownloadUrlForLayer"
   "ecr:GetLifecyclePolicy"
   "ecr:GetLifecyclePolicyPreview"
+  "ecr:GetRepositoryPolicy"
+  "ecr:ListImages"
   "ecr:ListTagsForResource"
-  "ecr:DescribeImageScanFindings"
   ```
 
 :::{note}
 If you are running Fargate or Fargate Spot, you may need the following policies in addition to the listed above:
   ```json
+  "ec2:DescribeSubnets"
   "ecs:CreateCluster"
   "ecs:DeleteCluster"
   "ecs:DescribeClusters"
   "ecs:ListClusters"
-  "ec2:DescribeSubnets"
   ```
 :::
 
@@ -252,7 +253,7 @@ Container options may be passed in long form (e.g `--option value`) or short for
 
 Few examples:
 
-```groovy
+```nextflow
 containerOptions '--tmpfs /run:rw,noexec,nosuid,size=128 --tmpfs /app:ro,size=64'
 
 containerOptions '-e MYVAR1 --env MYVAR2=foo2 --env MYVAR3=foo3 --memory-swap 3240000 --memory-swappiness 20 --shm-size 16000000'
@@ -408,20 +409,6 @@ To do that, first create a **Job Definition** in the AWS Console (or by other me
 process.container = 'job-definition://your-job-definition-name'
 ```
 
-### Pipeline execution
-
-The pipeline can be launched either in a local computer or an EC2 instance. The latter is suggested for heavy or long-running workloads.
-
-Pipeline input data can be stored either locally or in an [S3](https://aws.amazon.com/s3/) bucket. The pipeline execution must specify an S3 bucket to store intermediate results with the `-bucket-dir` (`-b`) command line option. For example:
-
-```bash
-nextflow run my-pipeline -bucket-dir s3://my-bucket/some/path
-```
-
-:::{warning}
-The bucket path should include at least a top level directory name, e.g. `s3://my-bucket/work` rather than `s3://my-bucket`.
-:::
-
 ### Hybrid workloads
 
 Nextflow allows the use of multiple executors in the same workflow application. This feature enables the deployment of hybrid workloads in which some jobs are executed in the local computer or local computing cluster and some jobs are offloaded to AWS Batch.
@@ -429,13 +416,6 @@ Nextflow allows the use of multiple executors in the same workflow application.
 To enable this feature, use one or more {ref}`config-process-selectors` in your Nextflow configuration to apply the AWS Batch configuration to the subset of processes that you want to offload. For example:
 
 ```groovy
-aws {
-    region = 'eu-west-1'
-    batch {
-        cliPath = '/home/ec2-user/miniconda/bin/aws'
-    }
-}
-
 process {
     withLabel: bigTask {
         executor = 'awsbatch'
@@ -443,9 +423,27 @@ process {
         container = 'my/image:tag'
     }
 }
+
+aws {
+    region = 'eu-west-1'
+}
 ```
 
-With the above configuration, processes with the `bigTask` {ref}`process-label` will run on AWS Batch, while the remaining processes with run in the local computer.
+With the above configuration, processes with the `bigTask` {ref}`process-label` will run on AWS Batch, while the remaining processes will run in the local computer.
+
+Then launch the pipeline with the -bucket-dir option to specify an AWS S3 path for the jobs computed with AWS Batch and, optionally, the -work-dir to specify the local storage for the jobs computed locally:
+
+```bash
+nextflow run <script or project name> -bucket-dir s3://my-bucket/some/path
+```
+
+:::{warning}
+The AWS S3 path needs to contain at least one sub-directory (e.g. `s3://my-bucket/work` rather than `s3://my-bucket`).
+:::
+
+:::{note}
+Nextflow will automatically manage the transfer of input and output files between the local and cloud environments when using hybrid workloads.
+:::
 
 ### Volume mounts
 
@@ -541,7 +539,8 @@ See the AWS documentation for details how to create the required AWS Batch queue
 and the Batch Execution Role.
 
 :::{note}
-This feature requires the use {ref}`Wave <wave-page>` container provisioning service.
+Nextflow uses [s5cmd](https://github.com/peak/s5cmd) to download the task input data and upload the task outputs.
+To enable this capability, you need to enable the Wave service in the Nextflow configuration, as shown in the above example. See {ref}`Wave <wave-page>` documentation for more details.
 :::
 
 ## Advanced configuration
diff --git a/docs/azure.md b/docs/azure.md
index bc10940ff3..57787bd5bf 100644
--- a/docs/azure.md
+++ b/docs/azure.md
@@ -1,6 +1,6 @@
 (azure-page)=
 
-# Azure Cloud
+# Azure
 
 :::{versionadded} 21.04.0
 :::
@@ -155,7 +155,7 @@ Replacing `<PIPELINE NAME>` with a pipeline name e.g. `nextflow-io/rnaseq-nf` an
 
 See the [Batch documentation](https://docs.microsoft.com/en-us/azure/batch/quick-create-portal) for further details about the configuration for Azure Batch.
 
-### Pools configuration
+### Autopools
 
 When using the `autoPoolMode` option, Nextflow automatically creates a `pool` of compute nodes appropriate for your pipeline.
 
@@ -163,16 +163,16 @@ By default, the `cpus` and `memory` directives are used to find the smallest mac
 
 To specify multiple Azure machine families, use a comma separated list with glob (`*`) values in the `machineType` directive. For example, the following will select any machine size from D or E v5 machines, with additional data disk, denoted by the `d` suffix:
 
-```config
+```groovy
 process.machineType = "Standard_D*d_v5,Standard_E*d_v5"
 ```
 
-For example, the following process will create a pool of `Standard_E4d_v5` machines based when using `autoPoolMode`:
+For example, the following process will create a pool of `Standard_E8d_v5` machines based when using `autoPoolMode`:
 
 ```nextflow
 process EXAMPLE_PROCESS {
     machineType "Standard_E*d_v5"
-    cpus 16
+    cpus 8
     memory 8.GB
 
     script:
@@ -405,6 +405,53 @@ The value of the setting must be the identifier of a subnet available in the vir
 Batch Authentication with Shared Keys does not allow to link external resources (like Virtual Networks) to the pool. Therefore, Active Directory Authentication must be used in conjunction with the `virtualNetwork` setting.
 :::
 
+### Hybrid workloads
+
+Nextflow allows the use of multiple executors in the same workflow application. This feature enables the deployment of hybrid workloads in which some jobs are executed in the local computer or local computing cluster and some jobs are offloaded to Azure Batch.
+
+To enable this feature, use one or more {ref}`config-process-selectors` in your Nextflow configuration to apply the Azure Batch configuration to the subset of processes that you want to offload. For example:
+
+```groovy
+process {
+    withLabel: bigTask {
+        executor = 'azurebatch'
+        queue = 'my-batch-pool'
+        container = 'my/image:tag'
+    }
+}
+
+azure {
+    storage {
+        accountName = '<YOUR STORAGE ACCOUNT NAME>'
+        accountKey = '<YOUR STORAGE ACCOUNT KEY>'
+    }
+    batch {
+        location = '<YOUR LOCATION>'
+        accountName = '<YOUR BATCH ACCOUNT NAME>'
+        accountKey = '<YOUR BATCH ACCOUNT KEY>'
+    }
+}
+```
+
+With the above configuration, processes with the bigTask {ref}`process-label` will run on Azure Batch, while the remaining processes will run on the local computer.
+
+Then launch the pipeline with the `-bucket-dir` option to specify an Azure Blob Storage path for the jobs computed with Azure Batch, and optionally, use the `-work-dir` option to specify the local storage for the jobs computed locally:
+
+```bash
+nextflow run <script or project name> -bucket-dir az://my-container/some/path
+```
+
+:::{warning}
+The Azure Blob Storage path needs to contain at least one sub-directory (e.g. `az://my-container/work` rather than `az://my-container`).
+:::
+
+:::{note}
+Nextflow will automatically manage the transfer of input and output files between the local and cloud environments when using hybrid workloads.
+
+:::{tip}
+When using [Fusion](./fusion.md), the `-bucket-dir` option is not required. Fusion implements a distributed virtual file system that allows seamless access to Azure Blob Storage using a standard POSIX interface, enabling direct mounting of remote blob storage as if it were a local file system. This simplifies and speeds up most operations, bridging the gap between cloud-native storage and data analysis workflows.
+:::
+
 ## Microsoft Entra
 
 Using Microsoft Entra for role-based access control is more secure than using access keys and should be used wherever possible. You can authenticate to Azure Entra using a Managed Identity when running on resources within the Azure environment, or by authenticating as an Azure Service Principal when running on external resources.
diff --git a/docs/cache-and-resume.md b/docs/cache-and-resume.md
index 55b890ef43..7184909aa2 100644
--- a/docs/cache-and-resume.md
+++ b/docs/cache-and-resume.md
@@ -16,7 +16,7 @@ The task cache is used in conjunction with the [work directory](#work-directory)
 
 The task hash is computed from the following metadata:
 
-- Session ID (see `workflow.sessionId` in {ref}`metadata-workflow`)
+- Session ID (see `workflow.sessionId` in {ref}`stdlib-constants`)
 - Task name (see `name` in {ref}`trace-report`)
 - Task container image (if applicable)
 - Task {ref}`environment modules <process-module>` (if applicable)
@@ -112,9 +112,9 @@ While Nextflow tries to make it easy to write safe concurrent code, it is still
 
 Consider the following example:
 
-```groovy
-Channel.of(1,2,3) | map { it -> X=it; X+=2 } | view { "ch1 = $it" }
-Channel.of(1,2,3) | map { it -> X=it; X*=2 } | view { "ch2 = $it" }
+```nextflow
+Channel.of(1,2,3) | map { v -> X=v; X+=2 } | view { v -> "ch1 = $v" }
+Channel.of(1,2,3) | map { v -> X=v; X*=2 } | view { v -> "ch2 = $v" }
 ```
 
 The problem here is that `X` is declared in each `map` closure without the `def` keyword (or other type qualifier). Using the `def` keyword makes the variable local to the enclosing scope; omitting the `def` keyword makes the variable global to the entire script.
@@ -123,12 +123,12 @@ Because `X` is global, and operators are executed concurrently, there is a *race
 
 The solution is to not use a global variable where a local variable is enough (or in this simple example, avoid the variable altogether):
 
-```groovy
+```nextflow
 // local variable
-Channel.of(1,2,3) | map { it -> def X=it; X+=2 } | view { "ch1 = $it" }
+Channel.of(1,2,3) | map { v -> def X=v; X+=2 } | view { v -> "ch1 = $v" }
 
 // no variable
-Channel.of(1,2,3) | map { it -> it * 2 } | view { "ch2 = $it" }
+Channel.of(1,2,3) | map { v -> v * 2 } | view { v -> "ch2 = $v" }
 ```
 
 (cache-nondeterministic-inputs)=
@@ -137,7 +137,7 @@ Channel.of(1,2,3) | map { it -> it * 2 } | view { "ch2 = $it" }
 
 Sometimes a process needs to merge inputs from different sources. Consider the following example:
 
-```groovy
+```nextflow
 workflow {
     ch_foo = Channel.of( ['1', '1.foo'], ['2', '2.foo'] )
     ch_bar = Channel.of( ['2', '2.bar'], ['1', '1.bar'] )
@@ -148,6 +148,8 @@ process gather {
     input:
     tuple val(id), file(foo)
     tuple val(id), file(bar)
+
+    script:
     """
     merge_command $foo $bar
     """
@@ -158,7 +160,7 @@ It is tempting to assume that the process inputs will be matched by `id` like th
 
 The solution is to explicitly join the two channels before the process invocation:
 
-```groovy
+```nextflow
 workflow {
     ch_foo = Channel.of( ['1', '1.foo'], ['2', '2.foo'] )
     ch_bar = Channel.of( ['2', '2.bar'], ['1', '1.bar'] )
@@ -168,6 +170,8 @@ workflow {
 process gather {
     input:
     tuple val(id), file(foo), file(bar)
+
+    script:
     """
     merge_command $foo $bar
     """
diff --git a/docs/channel.md b/docs/channel.md
index 46616b0102..8eb4c1b576 100644
--- a/docs/channel.md
+++ b/docs/channel.md
@@ -22,7 +22,7 @@ In Nextflow there are two kinds of channels: *queue channels* and *value channel
 A *queue channel* is a non-blocking unidirectional FIFO queue connecting a *producer* process (i.e. outputting a value)
 to a consumer process, or an operators.
 
-A queue channel can be created by factory methods ([of](#of), [fromPath](#frompath), etc), operators ({ref}`operator-map`, {ref}`operator-flatmap`, etc), and processes (see {ref}`Process outputs <process-output>`).
+A queue channel can be created by factory methods ({ref}`channel-of`, {ref}`channel-path`, etc), operators ({ref}`operator-map`, {ref}`operator-flatmap`, etc), and processes (see {ref}`Process outputs <process-output>`).
 
 (channel-type-value)=
 
@@ -31,13 +31,13 @@ A queue channel can be created by factory methods ([of](#of), [fromPath](#frompa
 A *value channel* can be bound (i.e. assigned) with one and only one value, and can be consumed any number of times by
 a process or an operator.
 
-A value channel can be created with the [value](#value) factory method or by any operator that produces a single value
+A value channel can be created with the {ref}`channel-value` factory method or by any operator that produces a single value
 ({ref}`operator-first`, {ref}`operator-collect`, {ref}`operator-reduce`, etc). Additionally, a process will emit value
 channels if it is invoked with all value channels, including simple values which are implicitly wrapped in a value channel.
 
 For example:
 
-```groovy
+```nextflow
 process foo {
   input:
   val x
@@ -45,6 +45,7 @@ process foo {
   output:
   path 'x.txt'
 
+  script:
   """
   echo $x > x.txt
   """
@@ -52,7 +53,7 @@ process foo {
 
 workflow {
   result = foo(1)
-  result.view { "Result: ${it}" }
+  result.view { file -> "Result: ${file}" }
 }
 ```
 
@@ -61,500 +62,51 @@ wrapped in a value channel, and the output is also emitted as a value channel.
 
 See also: {ref}`process-multiple-input-channels`.
 
-(channel-factory)=
-
 ## Channel factories
 
-Channels may be created explicitly using the following channel factory methods.
-
-:::{versionadded} 20.07.0
-`channel` was introduced as an alias of `Channel`, allowing factory methods to be specified as `channel.of()` or
-`Channel.of()`, and so on.
-:::
-
-(channel-empty)=
-
-### empty
-
-The `channel.empty` factory method, by definition, creates a channel that doesn't emit any value.
-
-See also: {ref}`operator-ifempty`.
-
-(channel-from)=
-
-### from
-
-:::{deprecated} 19.09.0-edge
-Use [channel.of](#of) or [channel.fromList](#fromlist) instead.
-:::
-
-The `channel.from` method allows you to create a channel emitting any sequence of values that are specified as the method argument, for example:
-
-```groovy
-ch = channel.from( 1, 3, 5, 7 )
-ch.subscribe { println "value: $it" }
-```
-
-The first line in this example creates a variable `ch` which holds a channel object. This channel emits the values specified as a parameter in the `from` method. Thus the second line will print the following:
-
-```
-value: 1
-value: 3
-value: 5
-value: 7
-```
-
-The following example shows how to create a channel from a *range* of numbers or strings:
-
-```groovy
-zeroToNine = channel.from( 0..9 )
-strings = channel.from( 'A'..'Z' )
-```
-
-:::{note}
-When the `channel.from` argument is an object implementing the (Java) [Collection](http://docs.oracle.com/javase/7/docs/api/java/util/Collection.html) interface, the resulting channel emits the collection entries as individual items.
-:::
-
-Thus the following two declarations produce an identical result even though in the first case the items are specified as multiple arguments while in the second case as a single list object argument:
+Channel factories are functions that can create channels.
 
-```groovy
-channel.from( 1, 3, 5, 7, 9 )
-channel.from( [1, 3, 5, 7, 9] )
-```
-
-But when more than one argument is provided, they are always managed as *single* emissions. Thus, the following example creates a channel emitting three entries each of which is a list containing two elements:
-
-```groovy
-channel.from( [1, 2], [5,6], [7,9] )
-```
+For example, the `Channel.of()` factory can be used to create a channel from an arbitrary list of arguments:
 
-(channel-fromlist)=
-
-### fromList
-
-:::{versionadded} 19.10.0
-:::
-
-The `channel.fromList` method allows you to create a channel emitting the values provided as a list of elements, for example:
-
-```groovy
-channel
-    .fromList( ['a', 'b', 'c', 'd'] )
-    .view { "value: $it" }
-```
-
-Prints:
-
-```
-value: a
-value: b
-value: c
-value: d
+```nextflow
+Channel.of(1, 2, 3).view()
 ```
 
-See also: [channel.of](#of) factory method.
-
-(channel-path)=
-
-### fromPath
-
-You can create a channel emitting one or more file paths by using the `channel.fromPath` method and specifying a path
-string as an argument. For example:
-
-```groovy
-myFileChannel = channel.fromPath( '/data/some/bigfile.txt' )
-```
-
-The above line creates a channel and binds it to a [Path](http://docs.oracle.com/javase/7/docs/api/java/nio/file/Path.html)
-object for the specified file.
-
-:::{note}
-`channel.fromPath` does not check whether the file exists.
-:::
-
-Whenever the `channel.fromPath` argument contains a `*` or `?` wildcard character it is interpreted as a [glob][glob] path matcher.
-For example:
-
-```groovy
-myFileChannel = channel.fromPath( '/data/big/*.txt' )
-```
-
-This example creates a channel and emits as many `Path` items as there are files with `txt` extension in the `/data/big` folder.
-
-:::{tip}
-Two asterisks, i.e. `**`, works like `*` but crosses directory boundaries. This syntax is generally used for matching complete paths. Curly brackets specify a collection of sub-patterns.
-:::
-
-For example:
-
-```groovy
-files = channel.fromPath( 'data/**.fa' )
-moreFiles = channel.fromPath( 'data/**/*.fa' )
-pairFiles = channel.fromPath( 'data/file_{1,2}.fq' )
-```
-
-The first line returns a channel emitting the files ending with the suffix `.fa` in the `data` folder *and* recursively in all its sub-folders. While the second one only emits the files which have the same suffix in *any* sub-folder in the `data` path. Finally the last example emits two files: `data/file_1.fq` and `data/file_2.fq`.
-
-:::{note}
-As in Linux Bash, the `*` wildcard does not catch hidden files (i.e. files whose name starts with a `.` character).
-:::
-
-Multiple paths or glob patterns can be specified using a list:
-
-```groovy
-channel.fromPath( ['/some/path/*.fq', '/other/path/*.fastq'] )
-```
-
-In order to include hidden files, you need to start your pattern with a period character or specify the `hidden: true` option. For example:
-
-```groovy
-expl1 = channel.fromPath( '/path/.*' )
-expl2 = channel.fromPath( '/path/.*.fa' )
-expl3 = channel.fromPath( '/path/*', hidden: true )
-```
-
-The first example returns all hidden files in the specified path. The second one returns all hidden files ending with the `.fa` suffix. Finally the last example returns all files (hidden and non-hidden) in that path.
-
-By default a [glob][glob] pattern only looks for regular file paths that match the specified criteria, i.e. it won't return directory paths.
-
-You can use the `type` option specifying the value `file`, `dir` or `any` in order to define what kind of paths you want. For example:
-
-```groovy
-myFileChannel = channel.fromPath( '/path/*b', type: 'dir' )
-myFileChannel = channel.fromPath( '/path/a*', type: 'any' )
-```
-
-The first example will return all *directory* paths ending with the `b` suffix, while the second will return any file or directory starting with a `a` prefix.
-
-Available options:
-
-`checkIfExists`
-: When `true` throws an exception of the specified path do not exist in the file system (default: `false`)
-
-`followLinks`
-: When `true` it follows symbolic links during directories tree traversal, otherwise they are managed as files (default: `true`)
-
-`glob`
-: When `true` interprets characters `*`, `?`, `[]` and `{}` as glob wildcards, otherwise handles them as normal characters (default: `true`)
-
-`hidden`
-: When `true` includes hidden files in the resulting paths (default: `false`)
-
-`maxDepth`
-: Maximum number of directory levels to visit (default: no limit)
-
-`relative`
-: When `true` returned paths are relative to the top-most common directory (default: `false`)
-
-`type`
-: Type of paths returned, either `file`, `dir` or `any` (default: `file`)
-
-(channel-filepairs)=
-
-### fromFilePairs
-
-The `channel.fromFilePairs` method creates a channel emitting the file pairs matching a [glob][glob] pattern provided
-by the user. The matching files are emitted as tuples in which the first element is the grouping key of the matching pair and the second element is the list of files (sorted in lexicographical order). For example:
-
-```groovy
-channel
-    .fromFilePairs('/my/data/SRR*_{1,2}.fastq')
-    .view()
-```
-
-It will produce an output similar to the following:
-
-```
-[SRR493366, [/my/data/SRR493366_1.fastq, /my/data/SRR493366_2.fastq]]
-[SRR493367, [/my/data/SRR493367_1.fastq, /my/data/SRR493367_2.fastq]]
-[SRR493368, [/my/data/SRR493368_1.fastq, /my/data/SRR493368_2.fastq]]
-[SRR493369, [/my/data/SRR493369_1.fastq, /my/data/SRR493369_2.fastq]]
-[SRR493370, [/my/data/SRR493370_1.fastq, /my/data/SRR493370_2.fastq]]
-[SRR493371, [/my/data/SRR493371_1.fastq, /my/data/SRR493371_2.fastq]]
-```
-
-:::{note}
-The glob pattern must contain at least one `*` wildcard character.
-:::
-
-Multiple glob patterns can be specified using a list:
-
-```groovy
-channel.fromFilePairs( ['/some/data/SRR*_{1,2}.fastq', '/other/data/QFF*_{1,2}.fastq'] )
-```
-
-Alternatively, it is possible to implement a custom file pair grouping strategy providing a closure which, given the current file as parameter, returns the grouping key. For example:
-
-```groovy
-channel
-    .fromFilePairs('/some/data/*', size: -1) { file -> file.extension }
-    .view { ext, files -> "Files with the extension $ext are $files" }
-```
-
-Available options:
-
-`checkIfExists`
-: When `true` throws an exception of the specified path do not exist in the file system (default: `false`)
-
-`followLinks`
-: When `true` it follows symbolic links during directories tree traversal, otherwise they are managed as files (default: `true`)
-
-`flat`
-: When `true` the matching files are produced as sole elements in the emitted tuples (default: `false`).
-
-`hidden`
-: When `true` includes hidden files in the resulting paths (default: `false`)
-
-`maxDepth`
-: Maximum number of directory levels to visit (default: no limit)
-
-`size`
-: Defines the number of files each emitted item is expected to hold (default: 2). Set to `-1` for any.
-
-`type`
-: Type of paths returned, either `file`, `dir` or `any` (default: `file`)
-
-(channel-fromsra)=
-
-### fromSRA
-
-:::{versionadded} 19.04.0
-:::
-
-The `channel.fromSRA` method queries the [NCBI SRA](https://www.ncbi.nlm.nih.gov/sra) database and returns a channel emitting the FASTQ files matching the specified criteria i.e project or accession number(s). For example:
-
-```groovy
-channel
-    .fromSRA('SRP043510')
-    .view()
-```
-
-It returns:
-
-```
-[SRR1448794, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/004/SRR1448794/SRR1448794.fastq.gz]
-[SRR1448795, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/005/SRR1448795/SRR1448795.fastq.gz]
-[SRR1448792, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/002/SRR1448792/SRR1448792.fastq.gz]
-[SRR1448793, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/003/SRR1448793/SRR1448793.fastq.gz]
-[SRR1910483, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/003/SRR1910483/SRR1910483.fastq.gz]
-[SRR1910482, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/002/SRR1910482/SRR1910482.fastq.gz]
-(remaining omitted)
-```
-
-Multiple accession IDs can be specified using a list object:
-
-```groovy
-ids = ['ERR908507', 'ERR908506', 'ERR908505']
-channel
-    .fromSRA(ids)
-    .view()
-```
-
-```
-[ERR908507, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908507/ERR908507_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908507/ERR908507_2.fastq.gz]]
-[ERR908506, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908506/ERR908506_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908506/ERR908506_2.fastq.gz]]
-[ERR908505, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908505/ERR908505_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908505/ERR908505_2.fastq.gz]]
-```
-
-:::{note}
-Each read pair is implicitly managed and returned as a list of files.
-:::
-
-This method uses the NCBI [ESearch](https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch) API behind the scenes, therefore it allows the use of any query term supported by this API.
-
-To access the ESearch API, you must provide your [NCBI API keys](https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities) through one of the following ways:
-
-- The `apiKey` option:
-  ```groovy
-  channel.fromSRA(ids, apiKey:'0123456789abcdef')
-  ```
-
-- The `NCBI_API_KEY` variable in your environment:
-  ```bash
-  export NCBI_API_KEY=0123456789abcdef
-  ```
-
-Available options:
-
-`apiKey`
-: NCBI user API key.
-
-`cache`
-: Enable/disable the caching API requests (default: `true`).
-
-`max`
-: Maximum number of entries that can be retried (default: unlimited) .
-
-`protocol`
-: Allow choosing the protocol for the resulting remote URLs. Available choices: `ftp`, `http`, `https` (default: `ftp`).
-
-(channel-interval)=
-
-### interval
-
-The `interval` method emits an incrementing index (starting from zero) at a periodic interval. For example:
-
-```groovy
-Channel.interval('1s').view()
-```
-
-The above snippet will emit 0, 1, 2, and so on, every second, forever. You can use an operator such as {ref}`operator-take` or {ref}`operator-until` to close the channel based on a stopping condition.
-
-An optional closure can be used to transform the index. Additionally, returning `Channel.STOP` will close the channel. For example:
-
-```groovy
-ch = Channel.interval('1s') { i ->
-    i == 10 ? Channel.STOP : i
-}
-ch.view()
-```
-
-(channel-of)=
-
-### of
-
-:::{versionadded} 19.10.0
-:::
-
-The `channel.of` method allows you to create a channel that emits the arguments provided to it, for example:
-
-```groovy
-ch = channel.of( 1, 3, 5, 7 )
-ch.view { "value: $it" }
-```
-
-The first line in this example creates a variable `ch` which holds a channel object. This channel emits the arguments
-supplied to the `of` method. Thus the second line prints the following:
-
-```
-value: 1
-value: 3
-value: 5
-value: 7
-```
-
-Ranges of values are expanded accordingly:
-
-```groovy
-channel
-    .of(1..23, 'X', 'Y')
-    .view()
-```
-
-Prints:
-
-```
-1
-2
-3
-4
-:
-23
-X
-Y
-```
-
-See also: [channel.fromList](#fromlist) factory method.
-
-(channel-topic)=
-
-### topic
-
-:::{versionadded} 23.11.0-edge
-:::
-
-:::{note}
-This feature requires the `nextflow.preview.topic` feature flag to be enabled.
-:::
-
-A *topic channel* is a queue channel that can receive values from many source channels *implicitly* based on a matching *topic name*.
-
-:::{tip}
-You can think about it as a channel that is shared across many different process using the same *topic name*.
-:::
-
-A process output can be assigned to a topic using the `topic` option on an output, for example:
-
-```groovy
-process foo {
-  output:
-  val('foo'), topic: my_topic
-}
-
-process bar {
-  output:
-  val('bar'), topic: my_topic
-}
-```
-
-The `channel.topic` method allows referencing the topic channel with the specified name, which can be used as a process
-input or operator composition as any other Nextflow channel:
-
-```groovy
-channel.topic('my-topic').view()
-```
-
-This approach is a convenient way to collect related items from many different sources without explicitly connecting them (e.g. using the `mix` operator).
-
-:::{warning}
-Any process that consumes a topic channel (directly or indirectly) should not send any outputs to that topic, or else the pipeline will hang forever.
+:::{versionadded} 20.07.0
+`channel` was introduced as an alias of `Channel`, allowing factory methods to be specified as `channel.of()` or `Channel.of()`, and so on.
 :::
 
-See also: {ref}`process-additional-options` for process outputs.
-
-(channel-value)=
-
-### value
-
-The `channel.value` method is used to create a value channel. An optional (not `null`) argument can be specified to bind
-the channel to a specific value. For example:
-
-```groovy
-expl1 = channel.value()
-expl2 = channel.value( 'Hello there' )
-expl3 = channel.value( [1,2,3,4,5] )
-```
-
-The first line in the example creates an 'empty' variable. The second line creates a channel and binds a string to it.
-The third line creates a channel and binds a list object to it that will be emitted as a single value.
-
-(channel-watchpath)=
+See {ref}`channel-factory` for the full list of channel factories.
 
-### watchPath
+## Operators
 
-The `channel.watchPath` method watches a folder for one or more files matching a specified pattern. As soon as there
-is a file that meets the specified condition, it is emitted over the channel that is returned by the `watchPath` method.
-The condition on files to watch can be specified by using `*` or `?` wildcard characters i.e. by specifying a [glob][glob] path matching criteria.
+Operators are methods that consume and produce channels. Because channels are asynchronous, operators are necessary to manipulate the values in a channel, without using a process. As a result, operators are useful for implementing the "glue logic" between processes.
 
-For example:
+See {ref}`operator-page` for the full list of operators. If you are new to Nextflow, here are some commonly-used operators to learn first:
 
-```groovy
-channel
-    .watchPath( '/path/*.fa' )
-    .subscribe { println "Fasta file: $it" }
-```
+Filtering:
 
-By default it watches only for new files created in the specified folder. Optionally, it is possible to provide a second
-argument that specifies what event(s) to watch. The supported events are:
+- {ref}`operator-filter`: select all values in a channel that satisfy a condition
+- {ref}`operator-first`: select the first value in a channel
+- {ref}`operator-take`: select the first *n* values in a channel
+- {ref}`operator-unique`: select the unique values in a channel (i.e. remove duplicates)
 
-- `create`: A new file is created (default)
-- `modify`: A file is modified
-- `delete`: A file is deleted
+Transforming:
 
-You can specify more than one of these events by using a comma separated string as shown below:
+- {ref}`operator-collect`: collect the values from a channel into a list
+- {ref}`operator-grouptuple`: group the values from a channel based on a grouping key
+- {ref}`operator-map`: transform each value from a channel with a mapping function
+- {ref}`operator-reduce`: accumulate each value from a channel into a single value
 
-```groovy
-channel
-    .watchPath( '/path/*.fa', 'create,modify' )
-    .subscribe { println "File created or modified: $it" }
-```
+Combining multiple channels:
 
-:::{warning}
-The `channel.watchPath` factory waits endlessly for files that match the specified pattern and event(s), which means
-that it will cause your pipeline to run forever. Consider using the `take` or `until` operator to close the channel when
-a certain condition is met (e.g. after receiving 10 files, receiving a file named `DONE`).
-:::
+- {ref}`operator-combine`: emit the combinations of two channels
+- {ref}`operator-concat`: emit the values from multiple channels (in the order in which the channels were given)
+- {ref}`operator-join`: join the values from two channels based on a matching key
+- {ref}`operator-mix`: emit the values from multiple channels (in the order in which items arrive)
 
-See also: [channel.fromPath](#frompath) factory method.
+Miscellaneous:
 
-[glob]: http://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob
+- {ref}`operator-ifempty`: emit a channel, or a default value if the channel is empty
+- {ref}`operator-set`: assign a channel to a variable
+- {ref}`operator-view`: print each value in a channel to standard output
diff --git a/docs/cli.md b/docs/cli.md
index df93409d7d..a6d0b24544 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -1,60 +1,16 @@
 (cli-page)=
 
-# Command line interface (CLI)
+# Command line
 
-Nextflow provides a robust command line interface for the management and execution pipelines.
+Nextflow provides a robust command line interface (CLI) for the management and execution pipelines.
 
-Simply run `nextflow` with no options or `nextflow -h` to see the list of available top-level options and commands.
-
-(cli-options)=
-
-## Options
-
-The top-level options are meant to be invoked in relation to the core Nextflow application and are applied to all commands. For options specific to any command, refer the CLI Commands section.
+Simply run `nextflow` with no options or `nextflow -h` to see the list of available top-level options and commands. See {ref}`cli-reference` for the full list of subcommands with examples.
 
 :::{note}
 Nextflow options use a single dash prefix, e.g. `-foo`. Do not confuse with double dash notation, e.g. `--foo`, which is instead used for {ref}`Pipeline parameters <cli-params>`.
 :::
 
-Available options:
-
-`-C`
-: Use the specified configuration file(s) overriding any defaults.
-
-`-D`
-: Set JVM properties.
-
-`-bg`
-: Execute nextflow in background.
-
-`-c, -config`
-: Add the specified file to configuration set.
-
-`-d, -dockerize`
-: :::{deprecated} 23.09.0-edge
-  :::
-: Launch nextflow via Docker (experimental).
-
-`-h`
-: Print this help.
-
-`-log`
-: Set nextflow log file path.
-
-`-q, -quiet`
-: Do not print information messages.
-
-`-remote-debug`
-: Enable JVM interactive remote debugging (experimental).
-
-`-syslog`
-: Send logs to syslog server (e.g. localhost:514).
-
-`-trace`
-: Enable trace level logging for the specified packages. Multiple packages can be provided separating them with a comma, e.g. `-trace nextflow,io.seqera`.
-
-`-v, -version`
-: Print the program version.
+## Basic usage
 
 ### Hard configuration override
 
@@ -68,7 +24,7 @@ The `-C` option is used to override *all* settings specified in the default conf
 
 - Override **any** default configuration with a custom configuration file:
 
-  ```
+  ```console
   $ nextflow -C my.config run nextflow-io/hello
   ```
 
@@ -122,27 +78,6 @@ The `-c` option is used to append a new configuration to the default configurati
   $ nextflow -c nxf.config run nextflow-io/hello
   ```
 
-### Docker driven execution
-
-:::{deprecated} 23.09.0-edge
-:::
-
-Launch Nextflow via Docker.
-
-```console
-$ nextflow -dockerize COMMAND [arg...]
-```
-
-The `-dockerize` option is used to invoke the execution of Nextflow within a Docker container itself without installing a Java VM in the hosting environment.
-
-This option is *not* needed to run containerised pipeline jobs. For invoking a pipeline with the `docker` profile or executor, please refer to the `-with-docker` options in the `run` command. When using the `-dockerize` option in combination with containerized tasks, Nextflow will launch the tasks as sibling containers in the host environment (i.e. no Docker-in-Docker).
-
-- Invoke `nextflow` as a Docker container to execute a pipeline:
-
-  ```console
-  $ nextflow -dockerize run nextflow-io/hello
-  ```
-
 ### Help
 
 Print the help message.
@@ -213,14 +148,14 @@ The `-v` option prints out information about Nextflow, such as the version and b
 
 - The short version:
 
-  ```
+  ```console
   $ nextflow -v
   nextflow version 20.07.1.5412
   ```
 
 - The full version info with citation and website link:
 
-  ```
+  ```console
   $ nextflow -version
   N E X T F L O W
   version 20.07.1 build 5412
@@ -229,1289 +164,199 @@ The `-v` option prints out information about Nextflow, such as the version and b
   http://nextflow.io
   ```
 
-(cli-commands)=
-
-## Commands
-
-(cli-clean)=
-
-### clean
-
-Clean up *cache* and *work* directories.
-
-**Usage**
-
-```console
-$ nextflow clean [run_name|session_id] [options]
-```
-
-**Description**
-
-Upon invocation within a directory, `nextflow` creates a project specific `.nextflow.log` file, `.nextflow` cache directory as well as a `work` directory. The `clean` command is designed to facilitate removal of these files from previous executions. A list of run names and session ids can be generated by invoking `nextflow log -q`.
-
-If no run name or session id is provided, it will clean the latest run.
-
-**Options**
-
-`-after`
-: Clean up runs executed *after* the specified one.
-
-`-before`
-: Clean up runs executed *before* the specified one.
-
-`-but`
-: Clean up all runs *except* the specified one.
-
-`-n, -dry-run`
-: Print names of files to be removed without deleting them.
-
-`-f, -force`
-: Force clean command.
-
-`-h, -help`
-: Print the command usage.
-
-`-k, -keep-logs`
-: Removes only temporary files but retains execution log entries and metadata.
-
-`-q, -quiet`
-: Do not print names of files removed.
-
-**Examples**
-
-Dry run to remove work directories for the run name `boring_euler`:
-
-```console
-$ nextflow clean boring_euler -n
-
-Would remove work/92/c1a9cd9a96e0531d81ca69f5dc3bb7
-Would remove work/3f/70944c7a549b6221e1ccc7b4b21b62
-Would remove work/0e/2ebdba85f76f6068b21a1bcbf10cab
-```
-
-Remove work directories for the run name `boring_euler`.
-
-```console
-$ nextflow clean boring_euler -f
-
-Removed work/92/c1a9cd9a96e0531d81ca69f5dc3bb7
-Removed work/3f/70944c7a549b6221e1ccc7b4b21b62
-Removed work/0e/2ebdba85f76f6068b21a1bcbf10cab
-```
-
-Remove the execution entries *except* for a specific execution.
-
-```console
-$ nextflow clean -but tiny_leavitt -f
-
-Removed work/1f/f1ea9158fb23b53d5083953121d6b6
-Removed work/bf/334115deec60929dc18edf0010032a
-Removed work/a3/06521d75da296d4dd7f4f8caaddad8
-```
-
-Dry run to remove the execution data *before* a specific execution.
-
-```console
-$ nextflow clean -before tiny_leavitt -n
-
-Would remove work/5d/ad76f7b7ab3500cf616814ef644b61
-Would remove work/c4/69a82b080a477612ba8d8e4c27b579
-Would remove work/be/a4fa2aa38f76fd324958c81c2e4603
-Would remove work/54/39116773891c47a91e3c1733aad4de
-```
-
-Dry run to remove the execution data *after* a specific execution.
-
-```console
-$ nextflow clean -after focused_payne -n
-
-Would remove work/1f/f1ea9158fb23b53d5083953121d6b6
-Would remove work/bf/334115deec60929dc18edf0010032a
-Would remove work/a3/06521d75da296d4dd7f4f8caaddad8
-```
-
-Dry run to remove the temporary execution data for a specific execution, while keeping the log files.
-
-```console
-$ nextflow clean -keep-logs tiny_leavitt -n
-
-Would remove temp files from work/1f/f1ea9158fb23b53d5083953121d6b6
-Would remove temp files from work/bf/334115deec60929dc18edf0010032a
-Would remove temp files from work/a3/06521d75da296d4dd7f4f8caaddad8
-```
-
-### clone
-
-Clone a remote project into a folder.
-
-**Usage**
-
-```console
-$ nextflow clone [options] [project]
-```
-
-**Description**
-
-The `clone` command downloads a pipeline from a Git-hosting platform into the *current directory* and modifies it accordingly. For downloading a pipeline into the global cache `~/.nextflow/assets`, please refer to the `nextflow pull` command.
-
-**Options**
-
-`-d, -deep`
-: Create a shallow clone of the specified depth.
-
-`-h, -help`
-: Print the command usage.
-
-`-hub` (`github`)
-: Service hub where the project is hosted. Options: `gitlab` or `bitbucket`.
-
-`-r` (`master`)
-: Revision to clone - It can be a git branch, tag, or revision number.
-
-`-user`
-: Private repository user name.
-
-**Examples**
-
-Clone the latest revision of a pipeline.
-
-```console
-$ nextflow clone nextflow-io/hello
-nextflow-io/hello cloned to: hello
-```
-
-Clone a specific revision of a pipeline.
-
-```console
-$ nextflow clone nextflow-io/hello -r v1.1
-nextflow-io/hello cloned to: hello
-```
-
-### config
-
-Print the resolved pipeline configuration.
-
-**Usage**
-
-```console
-$ nextflow config [options] [project name or path]
-```
-
-**Description**
-
-The `config` command is used for printing the project's configuration i.e. the `nextflow.config` and is especially useful for understanding the resolved profiles and parameters that Nextflow will use run a pipeline. For in-depth information, please refer the {ref}`config-profiles` section.
-
-**Options**
-
-`-flat`
-: Print config using flat notation.
-
-`-h, -help`
-: Print the command usage.
-
-`-profile`
-: Choose a configuration profile.
-
-`-properties`
-: Print config using Java properties notation.
-
-`-a, -show-profiles`
-: Show all configuration profiles.
-
-`-sort`
-: Sort config attributes.
-
-`-value`
-: :::{versionadded} 23.08.0-edge
-  :::
-: Print the value of a config option, or fail if the option is not defined.
-
-**Examples**
-
-Print out the inferred config using a the default group key-value notation.
-
-```console
-$ nextflow config
-
-docker {
-    enabled = true
-}
-
-process {
-    executor = 'local'
-}
-```
-
-Print out the config using a flat notation.
-
-```console
-$ nextflow config -flat
-
-docker.enabled = true
-process.executor = 'local'
-```
-
-Print out the config using the Java properties notation.
-
-```console
-$ nextflow config -properties
-
-docker.enabled = true
-process.executor = local
-```
-
-Print out the value of a specific configuration property.
+## Running pipelines
 
-```console
-$ nextflow config -value process.executor
-local
-```
-
-Print out all profiles from the project's configuration.
-
-```console
-$ nextflow config -show-profiles
-
-docker {
-    enabled = true
-}
-
-profiles {
-    standard {
-        process {
-            executor = 'local'
-        }
-    }
-    cloud {
-        process {
-            executor = 'cirrus'
-            container = 'cbcrg/imagex'
-        }
-    }
-}
-```
+The main purpose of the Nextflow CLI is to run Nextflow pipelines with the `run` command. Nextflow can execute a local script (e.g. `./main.nf`) or a remote project (e.g. `github.com/foo/bar`).
 
-(cli-console)=
+### Launching a remote project
 
-### console
+To launch the execution of a pipeline project, hosted in a remote code repository, you simply need to specify its qualified name or the repository URL after the `run` command. The qualified name is formed by two parts: the `owner` name and the `repository` name separated by a `/` character.
 
-Launch the Nextflow interactive console.
+In other words if a Nextflow project is hosted, for example, in a GitHub repository at the address `http://github.com/foo/bar`, it can be executed by entering the following command in your shell terminal:
 
-**Usage**
-
-```console
-$ nextflow console
+```bash
+nextflow run foo/bar
 ```
 
-**Description**
-
-The `console` command provides a Graphical User Interface (GUI) and an interactive REPL (Read-Eval-Print-Loop) for quick experimentation.
-
-**Options**
-
-None available
+or using the project URL:
 
-**Examples**
-
-Launch the `console` GUI.
-
-```console
-$ nextflow console
+```bash
+nextflow run http://github.com/foo/bar
 ```
 
-### drop
+If the project is found, it will be automatically downloaded to the Nextflow home directory (`$HOME/.nextflow` by default) and cached for subsequent runs.
 
-Delete the local copy of a project.
+:::{note}
+You must use the `-hub` option to specify the hosting service if your project is hosted on a service other than GitHub, e.g. `-hub bitbucket`. However, the `-hub` option is not required if you use the project URL.
+:::
 
-**Usage**
+Try this feature by running the following command:
 
-```console
-$ nextflow drop [options] [project]
+```bash
+nextflow run nextflow-io/hello
 ```
 
-**Description**
+It will download a trivial example from the repository published at <http://github.com/nextflow-io/hello> and execute it on your computer.
 
-The `drop` command is used to remove the projects which have been downloaded into the global cache. Please refer the `list` command for generating a list of downloaded pipelines.
+If the `owner` is omitted, Nextflow will search your cached pipelines for a pipeline that matches the name specified. If no pipeline is found, Nextflow will try to download it using the `organization` name defined by the `NXF_ORG` environment variable (`nextflow-io` by default ).
 
-**Options**
-
-`-f`
-: Delete the repository without taking care of local changes.
-
-`-h, -help`
-: Print the command usage.
-
-**Examples**
-
-Drop the `nextflow-io/hello` project.
+:::{tip}
+To access a private repository, specify the access credentials using the `-user` command line option. Then follow the interactive prompts to enter your password. Alternatively, define your private repository access credentials using Git. See {ref}`Git configuration <git-page>` for more information.
+:::
 
-```console
-$ nextflow drop nextflow-io/hello
-```
+### Using a specific revision
 
-Forcefully drop the `nextflow-io/hello` pipeline, ignoring any local changes.
+Any Git branch, tag, or commit of a project repository can be used when launching a pipeline by specifying the `-r` option:
 
 ```console
-$ nextflow drop nextflow-io/hello -f
-```
+$ nextflow run nextflow-io/hello -r mybranch
 
-### fs
-
-Perform basic filesystem operations.
-
-**Usage**
+or
 
 ```console
-$ nextflow fs [subcommands]
+$ nextflow run nextflow-io/hello -r v1.1
 ```
 
-**Description**
-
-The `fs` command is used to perform filesystem operations like copy, move, delete, list directory, etc. Like the `file()` method, it can work with local files, remote URLs, and remote object storage. Storage credentials can be provided through the same manner as launching a pipeline (Nextflow config, environment vars, etc).
-
-**Options**
-
-`-h, -help`
-: Print the command usage.
-
-**Examples**
-
-List a directory.
-
-```console
-$ nextflow fs list <directory>
-```
+These commands will execute two different project revisions based on the given Git branch/tag/commit.
 
-Print the contents of a file to standard output.
+(cli-params)=
 
-```console
-$ nextflow fs cat <file>
-```
+### Pipeline parameters
 
-Copy a file or directory.
+Pipeline scripts can use an arbitrary number of parameters that can be overridden using the command line or Nextflow configuration files. Any script parameter can be specified on the command line by prefixing the parameter name with double-dash characters. For example:
 
 ```console
-$ nextflow fs cp <source> <target>
+$ nextflow run <pipeline> --foo Hello
 ```
 
-Move a file or directory.
+Then, the parameter can be accessed in the pipeline script using the `params.foo` identifier.
 
-```console
-$ nextflow fs mv <source> <target>
-```
+:::{note}
+When the parameter name is formatted using `camelCase`, a second parameter is created with the same value using `kebab-case`, and vice versa.
+:::
 
-Delete a file or directory.
+:::{warning}
+When a command line parameter includes one or more glob characters, i.e. wildcards like `*` or `?`, the parameter value must be enclosed in quotes to prevent Bash expansion and preserve the glob characters. For example:
 
 ```console
-$ nextflow fs rm <path>
+$ nextflow run <pipeline> --files "*.fasta"
 ```
-
-:::{versionadded} 23.10.0
 :::
 
-Print file or directory attributes.
+Parameters specified on the command line can be also specified in a params file using the `-params-file` option.
 
-```console
-$ nextflow fs stat <path>
+```bash
+nextflow run main.nf -params-file pipeline_params.yml
 ```
 
-### help
+The `-params-file` option loads parameters for your Nextflow pipeline from a JSON or YAML file. Parameters defined in the file are equivalent to specifying them directly on the command line. For example, instead of specifying parameters on the command line:
 
-Print the top-level help or specific help for a command.
-
-**Usage**
-
-```console
-$ nextflow help [options] [command]
+```bash
+nextflow run main.nf --alpha 1 --beta foo
 ```
 
-**Description**
-
-The `help` command prints out the overview of the CLI interface and enumerates the top-level *options* and *commands*. Note that this command is equivalent to simply invoking `nextflow` at the command line.
-
-**Options**
-
-`-h, -help`
-: Print the command usage.
-
-**Examples**
+Parameters can be represented in YAML format:
 
-Invoke the `help` option for the `drop` command.
-
-```console
-$ nextflow help drop
-
-Delete the local copy of a project
-Usage: drop [options] name of the project to drop
-   Options:
-     -f
-          Delete the repository without taking care of local changes
-          Default: false
-     -h, -help
-          Print the command usage
-          Default: false
+```yaml
+alpha: 1
+beta: 'foo'
 ```
 
-### info
-
-Print project or system runtime information.
-
-**Usage**
+Or in JSON format:
 
-```console
-$ nextflow info [options] [project]
+```json
+{
+  "alpha": 1,
+  "beta": "foo"
+}
 ```
 
-**Description**
-
-The `info` command prints out the nextflow runtime information about the hardware as well as the software versions of the Nextflow version and build, operating system, and Groovy and Java runtime. It can also be used to display information about a specific project.
-
-If no run name or session id is provided, it will clean the latest run.
+The parameters specified in a params file are merged with the resolved configuration. The values provided via a params file overwrite those of the same name in the Nextflow configuration file, but not those specified on the command line.
 
-**Options**
+## Managing projects
 
-`-u, -check-updates`
-: Check for remote updates.
+Nextflow seamlessly integrates with popular Git providers, including [BitBucket](http://bitbucket.org/), [GitHub](http://github.com), and [GitLab](http://gitlab.com) for managing Nextflow pipelines as version-controlled Git repositories.
 
-`-d`
-: Show detailed information.
+The following commands allow you to perform basic operations to manage your projects.
 
-`-h, -help`
-: Print the command usage.
+### Listing available projects
 
-`-o` (`text`)
-: Output format, either `text`, `json` or `yaml`.
+The `list` command allows you to list all the projects you have downloaded in your computer. For example:
 
-**Examples**
-
-Display Nextflow runtime and system info:
-
-```console
-$ nextflow info
-
-  Version: 20.07.1 build 5412
-  Created: 24-07-2020 15:18 UTC (20:48 IDT)
-  System: Mac OS X 10.15.6
-  Runtime: Groovy 2.5.11 on OpenJDK 64-Bit Server VM 1.8.0_192-b01
-  Encoding: UTF-8 (UTF-8)
+```bash
+nextflow list
 ```
 
-Display information about a specific project:
+This prints a list similar to the following:
 
-```console
-$ nextflow info nextflow-io/hello
-
-  project name: nextflow-io/hello
-  repository  : https://github.com/nextflow-io/hello
-  local path  : /Users/evanfloden/.nextflow/assets/nextflow-io/hello
-  main script : main.nf
-  revisions   :
-  * master (default)
-    mybranch
-    testing
-    v1.1 [t]
-    v1.2 [t]
 ```
-
-### inspect
-
-:::{versionadded} 23.09.0-edge
-:::
-
-Inspect process settings in a pipeline project. Currently only supports the `container` directive.
-
-**Usage**
-
-```console
-$ nextflow inspect [options] [project]
+cbcrg/ampa-nf
+cbcrg/piper-nf
+nextflow-io/hello
+nextflow-io/examples
 ```
 
-**Description**
-
-The `inspect` command allows you to determine the container for each process in a pipeline without running the pipeline. It prints to stdout a listing of containers for each process, formatted either as JSON or Nextflow configuration.
-
-**Options**
-
-`-concretize`
-: Build the container images resolved by the inspect command.
-
-`-format` (`json`)
-: Inspect output format. Can be `json` or `config`.
-
-`-i, -ignore-errors`
-: Ignore errors while inspecting the pipeline.
-
-`-params-file`
-: Load script parameters from a JSON/YAML file.
-
-`-profile`
-: Use the given configuration profile(s).
-
-`-r, revision`
-: Revision of the project to inspect (either a git branch, tag or commit SHA number).
-
-**Examples**
-
-Get the list of containers used by a pipeline.
+### Showing project information
 
-```console
-$ nextflow inspect nextflow-io/hello
-```
-
-Specify parameters as with the `run` command:
+By using the `info` command you can show information from a downloaded project. For example:
 
 ```console
-$ nextflow inspect main.nf --alpha 1 --beta foo
+$ nextflow info hello
+project name: nextflow-io/hello
+repository  : http://github.com/nextflow-io/hello
+local path  : $HOME/.nextflow/assets/nextflow-io/hello
+main script : main.nf
+revisions   :
+* master (default)
+  mybranch
+  v1.1 [t]
+  v1.2 [t]
 ```
 
-### kuberun
+Starting from the top it shows: the project name; the Git repository URL; the local directory where the project has been downloaded; the script that is executed when launched; the list of available revisions i.e. branches and tags. Tags are marked with a `[t]` on the right and the checked-out revision is marked with a `*` on the left.
 
-Launch a Nextflow pipeline on a Kubernetes cluster.
+### Pulling or updating a project
 
-**Usage**
+The `pull` command allows you to download a project from a GitHub repository or to update it if that repository has already been downloaded. For example:
 
 ```console
-$ nextflow kuberun [options] [project]
+$ nextflow pull nextflow-io/hello
 ```
 
-**Description**
-
-The `kuberun` command builds upon the `run` command and offers a deep integration with the Kubernetes execution environment. This command deploys the Nextflow runtime as a Kubernetes pod and assumes that you've already installed the `kubectl` CLI. The `kuberun` command does not allow the execution of local Nextflow scripts. For more information please refer to the {ref}`k8s-page` page.
-
-**Options**
-
-The `kuberun` command supports the following options from [`run`](#run):
-
-- `-cache`
-- `-disable-jobs-cancellation`
-- `-dsl1`
-- `-dsl2`
-- `-dump-channels`
-- `-dump-hashes`
-- `-e.<key>=<value>`
-- `-entry`
-- `-h, -help`
-- `-hub`
-- `-latest`
-- `-main-script`
-- `-name`
-- `-offline`
-- `-params-file`
-- `-plugins`
-- `-preview`
-- `-process.<key>=<value>`
-- `-profile`
-- `-qs, -queue-size`
-- `-resume`
-- `-r, -revision`
-- `-stub, -stub-run`
-- `-user`
-- `-with-conda`
-- `-with-dag`
-- `-N, -with-notification`
-- `-with-report`
-- `-with-spack`
-- `-with-timeline`
-- `-with-tower`
-- `-with-trace`
-- `-with-wave`
-- `-with-weblog`
-- `-without-spack`
-- `-without-wave`
-- `-w, -work-dir`
-
-The following new options are also available:
-
-`-head-cpus`
-: :::{versionadded} 22.01.0-edge
-  :::
-: Specify number of CPUs requested for the Nextflow pod.
-
-`-head-image`
-: :::{versionadded} 22.07.1-edge
-  :::
-: Specify the container image for the Nextflow driver pod.
-
-`-head-memory`
-: :::{versionadded} 22.01.0-edge
-  :::
-: Specify amount of memory requested for the Nextflow pod.
-
-`-head-prescript`
-: :::{versionadded} 22.05.0-edge
-  :::
-: Specify script to be run before the Nextflow pod starts.
-
-`-n, -namespace`
-: Specify the K8s namespace to use.
-
-`-remoteConfig`
-: Add the specified file from the K8s cluster to configuration set.
-
-`-remoteProfile`
-: Choose a configuration profile in the remoteConfig.
-
-`-v, -volume-mount`
-: Volume claim mounts, e.g. `my-pvc:/mnt/path`.
-
-**Examples**
-
-Execute a pipeline into a Kubernetes cluster.
+Alternatively, you can use the repository URL as the name of the project to pull:
 
 ```console
-$ nextflow kuberun nextflow-io/hello
+$ nextflow pull https://github.com/nextflow-io/hello
 ```
 
-### list
+Downloaded pipeline projects are stored in your directory `$HOME/.nextflow/assets` directory.
 
-List all downloaded projects.
+### Viewing the project code
 
-**Usage**
+The `view` command shows the content of the pipeline script you have pulled. For example:
 
 ```console
-$ nextflow list [options]
+$ nextflow view nextflow-io/hello
 ```
 
-**Description**
-
-The `list` commands prints a list of the projects which are already downloaded into the global cache `~/.nextflow/assets`.
-
-**Options**
-
-`-h, -help`
-: Print the command usage.
+By adding the `-l` option to the example above it will list the content of the repository.
 
-**Examples**
+### Cloning a project into a directory
 
-List the downloaded pipelines.
+The `clone` command allows you to copy a Nextflow pipeline project to a directory of your choice. For example:
 
 ```console
-$ nextflow list
-
-nextflow-io/hello
-nextflow-hub/fastqc
+$ nextflow clone nextflow-io/hello target-dir
 ```
 
-(cli-log)=
+If the destination directory is omitted the specified project is cloned to a directory with the same name as the pipeline base name (e.g. `hello`) in the current directory.
 
-### log
+The `clone` command can be used to inspect or modify the source code of a pipeline project. You can eventually commit and push back your changes by using the usual Git/GitHub workflow.
 
-Print the execution history and log information.
+### Deleting a project
 
-**Usage**
+Downloaded pipelines can be deleted by using the `drop` command, as shown below:
 
-```console
-$ nextflow log [options] [run_name | session_id]
+```bash
+nextflow drop nextflow-io/hello
 ```
-
-**Description**
-
-The `log` command is used to query the execution metadata associated with pipelines executed by Nextflow. The list of executed pipelines can be generated by running `nextflow log`. Instead of run name, it's also possible to use a session id. Moreover, this command contains multiple options to facilitate the queries and is especially useful while debugging a pipeline and while inspecting pipeline execution metadata.
-
-**Options**
-
-`-after`
-: Show log entries for runs executed *after* the specified one.
-
-`-before`
-: Show log entries for runs executed *before* the specified one.
-
-`-but`
-: Show log entries for runs executed *but* the specified one.
-
-`-f, -fields`
-: Comma-separated list of fields to include in the printed log. Use the `-l` option to see the list of available fields.
-
-`-F, -filter`
-: Filter log entries by a custom expression, e.g. `process =~ /foo.*/ && status == 'COMPLETED'`.
-
-`-h, -help`
-: Print the command usage.
-
-`-l, -list-fields`
-: Show all available fields.
-
-`-quiet`
-: Show only run names.
-
-`-s`
-: Character used to separate column values.
-
-`-t, -template`
-: Text template used to each record in the log.
-
-**Examples**
-
-Listing the execution logs of previous invocations of all pipelines in a project.
-
-```console
-$ nextflow log
-
-TIMESTAMP           DURATION        RUN NAME        STATUS  REVISION ID     SESSION ID                              COMMAND
-2020-10-07 11:52:24 2.1s            focused_payne   OK      96eb04d6a4      af6adaaa-ad4f-48a2-9f6a-b121e789adf5    nextflow run nextflow-io/hello -r master
-2020-10-07 11:53:00 3.1s            tiny_leavitt    OK      e3b475a61b      4d3b95c5-4385-42b6-b430-c865a70d56a4    nextflow run ./tutorial.nf
-2020-10-07 11:53:29 2.5s            boring_euler    OK      e3b475a61b      a6276975-7173-4208-ae09-ab9d6dce8737    nextflow run tutorial.nf
-```
-
-Listing only the *run names* of the execution logs of all pipelines invocations in a project.
-
-```console
-$ nextflow log -quiet
-
-focused_payne
-tiny_leavitt
-boring_euler
-```
-
-List the execution entries *only* a specific execution.
-
-```console
-$ nextflow log tiny_leavitt
-
-work/1f/f1ea9158fb23b53d5083953121d6b6
-work/bf/334115deec60929dc18edf0010032a
-work/a3/06521d75da296d4dd7f4f8caaddad8
-```
-
-List the execution entries *after* a specific execution.
-
-```console
-$ nextflow log -after tiny_leavitt
-
-work/92/c1a9cd9a96e0531d81ca69f5dc3bb7
-work/3f/70944c7a549b6221e1ccc7b4b21b62
-work/0e/2ebdba85f76f6068b21a1bcbf10cab
-```
-
-List the execution entries *before* a specific execution.
-
-```console
-$ nextflow log -before tiny_leavitt
-
-work/5d/ad76f7b7ab3500cf616814ef644b61
-work/c4/69a82b080a477612ba8d8e4c27b579
-work/be/a4fa2aa38f76fd324958c81c2e4603
-work/54/39116773891c47a91e3c1733aad4de
-```
-
-List the execution entries *except* for a specific execution.
-
-```console
-$ nextflow log -but tiny_leavitt
-
-work/5d/ad76f7b7ab3500cf616814ef644b61
-work/c4/69a82b080a477612ba8d8e4c27b579
-work/be/a4fa2aa38f76fd324958c81c2e4603
-work/54/39116773891c47a91e3c1733aad4de
-```
-
-Filter specific fields from the execution log of a process.
-
-```console
-$ nextflow log tiny_leavitt -f 'process,exit,hash,duration'
-
-splitLetters        0       1f/f1ea91       112ms
-convertToUpper      0       bf/334115       144ms
-convertToUpper      0       a3/06521d       139ms
-```
-
-Filter fields from the execution log of a process based on a criteria.
-
-```console
-$ nextflow log tiny_leavitt -F 'process =~ /splitLetters/'
-
-work/1f/f1ea9158fb23b53d5083953121d6b6
-```
-
-(cli-plugin)=
-
-### plugin
-
-Manage plugins and run plugin-specific commands.
-
-```console
-$ nextflow plugin <subcommand> [options]
-```
-
-The `plugin` command provides several subcommands for managing and using plugins:
-
-`install <plugin[@version],..>`
-
-: Install a plugin. Multiple plugins can be specified as a comma-separated list. Each plugin id consists of a name and optional version separated by a `@`.
-
-`<plugin>:<subcommand> [options]`
-
-: Execute a plugin-specific command.
-
-### pull
-
-Download or update a project.
-
-**Usage**
-
-```console
-$ nextflow pull [options] [project]
-```
-
-**Description**
-
-The `pull` command downloads a pipeline from a Git-hosting platform into the global cache `~/.nextflow/assets` and modifies it accordingly. For downloading a pipeline into a local directory, please refer to the `nextflow clone` command.
-
-**Options**
-
-`-all`
-: Update all downloaded projects.
-
-`-d, -deep`
-: Create a shallow clone of the specified depth.
-
-`-h, -help`
-: Print the command usage.
-
-`-hub` (`github`)
-: Service hub where the project is hosted. Options: `gitlab` or `bitbucket`
-
-`-r, -revision`
-: Revision of the project to run (either a git branch, tag or commit hash).
-: When passing a git tag or branch, the `workflow.revision` and `workflow.commitId` fields are populated. When passing only the commit hash, `workflow.revision` is not defined.
-
-`-user`
-: Private repository user name.
-
-**Examples**
-
-Download a new pipeline or pull the latest revision for a specific project.
-
-```console
-$ nextflow pull nextflow-io/hello
-
-Checking nextflow-io/hello ...
-done - revision: 96eb04d6a4 [master]
-```
-
-Pull the latest revision for all downloaded projects.
-
-```console
-$ nextflow pull -all
-
-Checking nextflow-io/hello ...
-done - revision: 96eb04d6a4 [master]
-Checking nextflow-hub/fastqc ...
-done - revision: 087659b18e [master]
-```
-
-Download a specific revision of a new project or pull the latest revision for a specific project.
-
-```console
-$ nextflow pull nextflow-io/hello -r v1.1
-
-Checking nextflow-io/hello ...
-checkout-out at AnyObjectId[1c3e9e7404127514d69369cd87f8036830f5cf64] - revision: 1c3e9e7404 [v1.1]
-```
-
-(cli-run)=
-
-### run
-
-Execute a pipeline.
-
-**Usage**
-
-```console
-$ nextflow run [options] [project]
-```
-
-**Description**
-
-The `run` command is used to execute a local pipeline script or remote pipeline project.
-
-**Options**
-
-`-E`
-: Exports all current system environment.
-
-`-ansi-log`
-: Enable/disable ANSI console logging.
-
-`-bucket-dir`
-: Remote bucket where intermediate result files are stored. When running a hybrid workflow, `-bucket-dir` and `-work-dir` should define separate work directories for remote tasks and local tasks, respectively.
-
-`-cache`
-: Enable/disable processes caching.
-
-`-d, -deep`
-: Create a shallow clone of the specified depth.
-
-`-disable-jobs-cancellation`
-: Prevent the cancellation of child jobs on execution termination
-
-`-dsl1`
-: :::{deprecated} 23.09.0-edge
-  :::
-: Execute the workflow using DSL1 syntax.
-
-`-dsl2`
-: :::{deprecated} 23.09.0-edge
-  :::
-: Execute the workflow using DSL2 syntax.
-
-`-dump-channels`
-: Dump channels for debugging purpose.
-
-`-dump-hashes`
-: Dump task hash keys for debugging purposes.
-: :::{versionadded} 23.10.0
-  You can use `-dump-hashes json` to dump the task hash keys as JSON for easier post-processing. See the {ref}`caching and resuming tips <cache-compare-hashes>` for more details.
-  :::
-
-`-e.<key>=<value>`
-: Add the specified variable to execution environment.
-
-`-entry`
-: Entry workflow to be executed.
-
-`-h, -help`
-: Print the command usage.
-
-`-hub` (`github`)
-: Service hub where the project is hosted. Options: `gitlab` or `bitbucket`
-
-`-latest`
-: Pull latest changes before run.
-
-`-lib`
-: Library extension path.
-
-`-main-script` (`main.nf`)
-: :::{versionadded} 20.09.1-edge
-  :::
-: The script file to be executed when launching a project directory or repository.
-
-`-name`
-: Assign a mnemonic name to the a pipeline run.
-
-`-offline`
-: Do not check for remote project updates.
-
-`-params-file`
-: Load script parameters from a JSON/YAML file.
-
-`-plugins`
-: Comma separated list of plugin ids to be applied in the pipeline execution.
-
-`-preview`
-: :::{versionadded} 22.06.0-edge
-  :::
-: Run the workflow script skipping the execution of all processes.
-
-`-process.<key>=<value>`
-: Set process config options.
-
-`-profile`
-: Choose a configuration profile.
-
-`-qs, -queue-size`
-: Max number of processes that can be executed in parallel by each executor.
-
-`-resume`
-: Execute the script using the cached results, useful to continue executions that was stopped by an error.
-
-`-r, -revision`
-: Revision of the project to run (either a git branch, tag or commit hash).
-: When passing a git tag or branch, the `workflow.revision` and `workflow.commitId` fields are populated. When passing only the commit hash, `workflow.revision` is not defined.
-
-`-stub-run, -stub`
-: Execute the workflow replacing process scripts with command stubs
-
-`-test`
-: Test a script function with the name specified.
-
-`-user`
-: Private repository user name.
-
-`-with-apptainer`
-: Enable process execution in an Apptainer container.
-
-`-with-charliecloud`
-: Enable process execution in a Charliecloud container.
-
-`-with-cloudcache`
-: Enable the use of the Cloud cache plugin for storing cache metadata to an object storage bucket.
-
-`-with-conda`
-: Use the specified Conda environment package or file (must end with `.yml` or `.yaml`)
-
-`-with-dag` (`dag-<timestamp>.html`)
-: Create pipeline DAG file.
-: :::{versionchanged} 23.10.0
-  The default format was changed from `dot` to `html`.
-  :::
-
-`-with-docker`
-: Enable process execution in a Docker container.
-
-`-N, -with-notification`
-: Send a notification email on workflow completion to the specified recipients.
-
-`-with-podman`
-: Enable process execution in a Podman container.
-
-`-with-report` (`report-<timestamp>.html`)
-: Create workflow execution HTML report.
-
-`-with-singularity`
-: Enable process execution in a Singularity container.
-
-`-with-spack`
-: Use the specified Spack environment package or file (must end with `.yaml`)
-
-`-with-timeline` (`timeline-<timestamp>.html`)
-: Create workflow execution timeline.
-
-`-with-tower` (`https://api.cloud.seqera.io`)
-: Monitor workflow execution with [Seqera Platform](https://seqera.io/) (formerly Tower Cloud).
-
-`-with-trace` (`trace-<timestamp>.txt`)
-: Create workflow execution trace file.
-
-`-with-wave` (`https://wave.seqera.io`)
-: Enable the use of Wave containers.
-
-`-with-weblog` (`http://localhost`)
-: Send workflow status messages via HTTP to target URL.
-
-`-without-conda`
-: Disable process execution with Conda.
-
-`-without-docker`
-: Disable process execution with Docker.
-
-`-without-podman`
-: Disable process execution in a Podman container.
-
-`-without-spack`
-: Disable process execution with Spack.
-
-`-without-wave`
-: Disable the use of Wave containers.
-
-`-w, -work-dir` (`work`)
-: Directory where intermediate result files are stored.
-
-**Examples**
-
-- Run a specific revision of a remote pipeline.
-
-  ```console
-  $ nextflow run nextflow-io/hello -r v1.1
-
-  N E X T F L O W  ~  version 20.07.1
-  Launching `nextflow-io/hello` [grave_cajal] - revision: 1c3e9e7404 [v1.1]
-  ```
-
-- Choose a `profile` for running the project. Assumes that a profile named `docker` has already been defined in the config file.
-
-  ```console
-  $ nextflow run main.nf -profile docker
-  ```
-
-- Execute a pipeline and generate the summary HTML report. For more information on the metrics, please refer the {ref}`tracing-page` section:
-
-  ```console
-  $ nextflow run main.nf -with-report
-  ```
-
-- Execute a pipeline with a custom queue size. By default, the queue size is the number of available CPUs.
-
-  ```console
-  $ nextflow run nextflow-io/hello -qs 4
-  ```
-
-- Invoke the pipeline with a specific workflow as the entry-point.
-
-  ```console
-  $ nextflow run main.nf -entry workflow_A
-  ```
-
-- Execute a pipeline with integrated monitoring in [Seqera Platform](https://seqera.io).
-
-  ```console
-  $ nextflow run nextflow-io/hello -with-tower
-  ```
-
-- Execute a pipeline with a custom parameters file (YAML or JSON).
-
-  ```console
-  $ nextflow run main.nf -params-file pipeline_params.yml
-  ```
-
-  For example, the following params file in YAML format:
-
-  ```yaml
-  alpha: 1
-  beta: 'foo'
-  ```
-
-  Or in JSON format:
-
-  ```json
-  {
-    "alpha": 1,
-    "beta": "foo"
-  }
-  ```
-
-  Is equivalent to the following command line:
-
-  ```console
-  $ nextflow run main.nf --alpha 1 --beta foo
-  ```
-
-  The parameters specified with this mechanism are merged with the resolved configuration (base configuration and profiles). The values provided via a params file overwrite those of the same name in the Nextflow configuration file.
-
-### self-update
-
-Update the nextflow runtime to the latest available version.
-
-**Usage**
-
-```console
-$ nextflow self-update
-```
-
-**Description**
-
-The `self-update` command directs the `nextflow` CLI to update itself to the latest stable release.
-
-**Examples**
-
-Update Nextflow.
-
-```console
-$ nextflow self-update
-
-      N E X T F L O W
-      version 20.07.1 build 5412
-      created 24-07-2020 15:18 UTC (20:48 IDT)
-      cite doi:10.1038/nbt.3820
-      http://nextflow.io
-
-
-Nextflow installation completed. Please note:
-- the executable file `nextflow` has been created in the folder: /usr/local/bin
-```
-
-### view
-
-View a project's script file(s).
-
-**Usage**
-
-```console
-$ nextflow view [options] [project]
-```
-
-**Description**
-
-The `view` command is used to inspect the pipelines that are already stored in the global nextflow cache. For downloading a pipeline into the global cache `~/.nextflow/assets`, refer to the `pull` command.
-
-**Options**
-
-`-h, -help`
-: Print the command usage.
-
-`-l`
-: List repository content.
-
-`-q`
-: Hide header line.
-
-**Examples**
-
-Viewing the contents of a downloaded pipeline.
-
-```console
-$ nextflow view nextflow-io/hello
-
-== content of file: .nextflow/assets/nextflow-io/hello/main.nf
-#!/usr/bin/env nextflow
-
-process sayHello {
-  input:
-    val x
-  output:
-    stdout
-  script:
-    """
-    echo '$x world!'
-    """
-}
-
-workflow {
-  Channel.of('Bonjour', 'Ciao', 'Hello', 'Hola') | sayHello | view
-}
-```
-
-List the folder structure of the downloaded pipeline:
-
-```console
-$ nextflow view -l nextflow-io/hello
-
-== content of path: .nextflow/assets/nextflow-io/hello
-LICENSE
-README.md
-nextflow.config
-.gitignore
-circle.yml
-foo.nf
-.git
-.travis.yml
-main.nf
-```
-
-View the contents of a downloaded pipeline without omitting the header:
-
-```console
-$ nextflow view -q nextflow-io/hello
-
-#!/usr/bin/env nextflow
-
-process sayHello {
-  input:
-    val x
-  output:
-    stdout
-  script:
-    """
-    echo '$x world!'
-    """
-}
-
-workflow {
-  Channel.of('Bonjour', 'Ciao', 'Hello', 'Hola') | sayHello | view
-}
-```
-
-(cli-params)=
-
-## Pipeline parameters
-
-Pipeline scripts can use an arbitrary number of parameters that can be overridden, either using the command line or the Nextflow configuration file. Any script parameter can be specified on the command line, prefixing the parameter name with double dash characters, e.g.:
-
-```bash
-nextflow run <my script> --foo Hello
-```
-
-Then, the parameter can be accessed in the pipeline script using the `params.foo` identifier.
-
-:::{note}
-When the parameter name is formatted using `camelCase`, a second parameter is created with the same value using `kebab-case`, and vice versa.
-:::
-
-:::{warning}
-When a command line parameter includes one or more glob characters, i.e. wildcards like `*` or `?`, the parameter value must be enclosed in quotes to prevent Bash expansion and preserve the glob characters. For example:
-
-```bash
-nextflow run <my script> --files "*.fasta"
-```
-:::
diff --git a/docs/conda.md b/docs/conda.md
index d3ea9ee56c..8c7405c1a4 100644
--- a/docs/conda.md
+++ b/docs/conda.md
@@ -6,7 +6,7 @@
 
 Nextflow has built-in support for Conda that allows the configuration of workflow dependencies using Conda recipes and environment files.
 
-This allows Nextflow applications to use popular tool collections such as [Bioconda](https://bioconda.github.io) whilst taking advantage of the configuration flexibility provided by Nextflow.
+This allows Nextflow applications to use popular tool collections such as [Bioconda](https://bioconda.github.io) and the [Python Package index](https://pypi.org/), whilst taking advantage of the configuration flexibility provided by Nextflow.
 
 ## Prerequisites
 
@@ -16,16 +16,16 @@ This feature requires the Conda or [Miniconda](https://conda.io/miniconda.html)
 
 Nextflow automatically creates and activates the Conda environment(s) given the dependencies specified by each process.
 
-Dependencies are specified by using the {ref}`process-conda` directive, providing either the names of the required Conda packages, the path of a Conda environment yaml file or the path of an existing Conda environment directory.
+Dependencies are specified by using the {ref}`process-conda` directive, providing either the names of the required Conda packages, the path of a Conda environment yaml file, or the path of an existing Conda environment directory.
 
 :::{note}
-Conda environments are stored on the file system. By default Nextflow instructs Conda to save the required environments in the pipeline work directory. Therefore the same environment can be created/saved multiple times across multiple executions when using a different work directory.
+Conda environments are stored on the file system. By default, Nextflow instructs Conda to save the required environments in the pipeline work directory. The same environment may be created/saved multiple times across multiple executions when using different work directories.
 :::
 
-You can specify the directory where the Conda environments are stored using the `conda.cacheDir` configuration property (see the {ref}`configuration page <config-conda>` for details). When using a computing cluster, make sure to use a shared file system path accessible from all compute nodes.
+You can specify the directory where the Conda environments are stored using the `conda.cacheDir` configuration property. When using a computing cluster, make sure to use a shared file system path accessible from all compute nodes. See the {ref}`configuration page <config-conda>` for details about Conda configuration.
 
 :::{warning}
-The Conda environment feature is not supported by executors that use remote object storage as a work directory e.g. AWS Batch.
+The Conda environment feature is not supported by executors that use remote object storage as a work directory. For example, AWS Batch.
 :::
 
 ### Enabling Conda environment
@@ -33,7 +33,7 @@ The Conda environment feature is not supported by executors that use remote obje
 :::{versionadded} 22.08.0-edge
 :::
 
-The use of Conda recipes specified using the {ref}`process-conda` directive needs to be enabled explicitly by setting the option shown below in the pipeline configuration file (i.e. `nextflow.config`):
+The use of Conda recipes specified using the {ref}`process-conda` directive needs to be enabled explicitly in the pipeline configuration file (i.e. `nextflow.config`):
 
 ```groovy
 conda.enabled = true
@@ -45,13 +45,14 @@ Alternatively, it can be specified by setting the variable `NXF_CONDA_ENABLED=tr
 
 Conda package names can specified using the `conda` directive. Multiple package names can be specified by separating them with a blank space. For example:
 
-```groovy
+```nextflow
 process foo {
   conda 'bwa samtools multiqc'
 
-  '''
+  script:
+  """
   your_command --here
-  '''
+  """
 }
 ```
 
@@ -61,6 +62,7 @@ The usual Conda package syntax and naming conventions can be used. The version o
 
 The name of the channel where a package is located can be specified prefixing the package with the channel name as shown here `bioconda::bwa=0.7.15`.
 
+(conda-env-files)=
 ### Use Conda environment files
 
 Conda environments can also be defined using one or more Conda environment files. This is a file that lists the required packages and channels structured using the YAML format. For example:
@@ -76,31 +78,18 @@ dependencies:
   - bwa=0.7.15
 ```
 
-This other example shows how to leverage a Conda environment file to install Python packages from the [PyPI repository](https://pypi.org/)), through the `pip` package manager (which must also be explicitly listed as a required package):
-
-```yaml
-name: my-env-2
-channels:
-  - defaults
-dependencies:
-  - pip
-  - pip:
-    - numpy
-    - pandas
-    - matplotlib
-```
-
 Read the Conda documentation for more details about how to create [environment files](https://conda.io/docs/user-guide/tasks/manage-environments.html#creating-an-environment-file-manually).
 
 The path of an environment file can be specified using the `conda` directive:
 
-```groovy
+```nextflow
 process foo {
   conda '/some/path/my-env.yaml'
 
-  '''
+  script:
+  """
   your_command --here
-  '''
+  """
 }
 ```
 
@@ -108,7 +97,26 @@ process foo {
 The environment file name **must** have a `.yml` or `.yaml` extension or else it won't be properly recognised.
 :::
 
-Alternatively, it is possible to provide the dependencies using a plain text file, just listing each package name as a separate line. For example:
+(conda-pypi)=
+### Python Packages from PyPI
+
+Conda environment files can also be used to install Python packages from the [PyPI repository](https://pypi.org/), through the `pip` package manager (which must also be explicitly listed as a required package):
+
+```yaml
+name: my-env-2
+channels:
+  - defaults
+dependencies:
+  - pip
+  - pip:
+    - numpy
+    - pandas
+    - matplotlib
+```
+
+### Conda text files
+
+It is possible to provide dependencies by listing each package name as a separate line in a plain text file. For example:
 
 ```
 bioconda::star=2.5.4a
@@ -120,17 +128,55 @@ bioconda::multiqc=1.4
 Like before, the extension matters. Make sure the dependencies file has a `.txt` extension.
 :::
 
+### Conda lock files
+
+The final way to provide packages to Conda is with [Conda lock files](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#identical-conda-envs).
+
+These are generated from existing Conda environments using the following command:
+
+```bash
+conda list --explicit > spec-file.txt
+```
+
+or if using Mamba / Micromamba:
+
+```bash
+micromamba env export --explicit > spec-file.txt
+```
+
+Conda lock files can also be downloaded from [Wave](https://seqera.io/wave/) build pages.
+
+These files include every package and their dependencies. As such, no Conda environment resolution step is needed. This is faster and more reproducible.
+
+The files contain package URLs and an optional md5hash for each download to confirm identity:
+
+```
+# micromamba env export --explicit
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
+# .. and so on
+```
+
+To use with Nextflow, simply set the `conda` directive to the lock file path.
+
 ### Use existing Conda environments
 
 If you already have a local Conda environment, you can use it in your workflow specifying the installation directory of such environment by using the `conda` directive:
 
-```groovy
+```nextflow
 process foo {
   conda '/path/to/an/existing/env/directory'
 
-  '''
+  script:
+  """
   your_command --here
-  '''
+  """
 }
 ```
 
diff --git a/docs/conf.py b/docs/conf.py
index fe58131005..f7f02e97d7 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -42,8 +42,11 @@
 myst_heading_anchors = 3
 
 rediraffe_redirects = {
-    'basic.md': 'overview.md',
     'getstarted.md': 'install.md',
+    'basic.md': 'overview.md',
+    'tracing.md': 'reports.md',
+    'mail.md': 'notifications.md',
+    'operator.md': 'reference/operator.md',
     'dsl2.md': 'dsl1.md'
 }
 
@@ -79,7 +82,7 @@
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-html_title = f"Nextflow v{release} documentation"
+html_title = f"Nextflow {release} documentation"
 
 # Get the current sha if not checked out at a specific version
 if len(release) == 0:
@@ -333,3 +336,77 @@
 
 # Allow duplicate toc entries.
 #epub_tocdup = True
+
+# see also: https://github.com/pygments/pygments/blob/master/pygments/lexers/jvm.py
+from pygments.lexer import RegexLexer
+from sphinx.highlighting import lexers
+
+class NextflowLexer(RegexLexer):
+    """
+    For Nextflow source code.
+    """
+
+    import re
+    from pygments.lexer import bygroups, using, this, default
+    from pygments.token import Comment, Operator, Keyword, Name, String, Number, Whitespace
+    from pygments.util import shebang_matches
+
+    name = 'Nextflow'
+    url = 'https://nextflow.io/'
+    aliases = ['nextflow', 'nf']
+    filenames = ['*.nf']
+    mimetypes = ['text/x-nextflow']
+    # version_added = '1.5'
+
+    flags = re.MULTILINE | re.DOTALL
+
+    tokens = {
+        'root': [
+            # Nextflow allows a file to start with a shebang
+            (r'#!(.*?)$', Comment.Preproc, 'base'),
+            default('base'),
+        ],
+        'base': [
+            (r'[^\S\n]+', Whitespace),
+            (r'(//.*?)(\n)', bygroups(Comment.Single, Whitespace)),
+            (r'/\*.*?\*/', Comment.Multiline),
+            # keywords: go before method names to avoid lexing "throw new XYZ"
+            # as a method signature
+            (r'(assert|catch|else|'
+             r'if|instanceof|new|return|throw|try|in|as)\b',
+             Keyword),
+            # method names
+            (r'^(\s*(?:[a-zA-Z_][\w.\[\]]*\s+)+?)'  # return arguments
+             r'('
+             r'[a-zA-Z_]\w*'                        # method name
+             r'|"(?:\\\\|\\[^\\]|[^"\\])*"'         # or double-quoted method name
+             r"|'(?:\\\\|\\[^\\]|[^'\\])*'"         # or single-quoted method name
+             r')'
+             r'(\s*)(\()',                          # signature start
+             bygroups(using(this), Name.Function, Whitespace, Operator)),
+            (r'@[a-zA-Z_][\w.]*', Name.Decorator),
+            (r'(def|enum|include|from|output|process|workflow)\b', Keyword.Declaration),
+            (r'(boolean|byte|char|double|float|int|long|short|void)\b',
+             Keyword.Type),
+            (r'(true|false|null)\b', Keyword.Constant),
+            (r'""".*?"""', String.Double),
+            (r"'''.*?'''", String.Single),
+            (r'"(\\\\|\\[^\\]|[^"\\])*"', String.Double),
+            (r"'(\\\\|\\[^\\]|[^'\\])*'", String.Single),
+            (r'/(\\\\|\\[^\\]|[^/\\])*/', String),
+            (r"'\\.'|'[^\\]'|'\\u[0-9a-fA-F]{4}'", String.Char),
+            (r'(\.)([a-zA-Z_]\w*)', bygroups(Operator, Name.Attribute)),
+            (r'[a-zA-Z_]\w*:', Name.Label),
+            (r'[a-zA-Z_$]\w*', Name),
+            (r'[~^*!%&\[\](){}<>|+=:;,./?-]', Operator),
+            (r'[0-9][0-9]*\.[0-9]+([eE][0-9]+)?[fd]?', Number.Float),
+            (r'0x[0-9a-fA-F]+', Number.Hex),
+            (r'[0-9]+L?', Number.Integer),
+            (r'\n', Whitespace)
+        ],
+    }
+
+    def analyse_text(text):
+        return shebang_matches(text, r'nextflow')
+
+lexers['nextflow'] = NextflowLexer()
diff --git a/docs/config.md b/docs/config.md
index e63aedd1dd..05fbc1130b 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -20,1316 +20,113 @@ When more than one of these options for specifying configurations are used, they
 You can use the `-C <config-file>` option to use a single configuration file and ignore all other files.
 :::
 
-### Config syntax
+(config-syntax)=
 
-A Nextflow configuration file is a simple text file containing a set of properties defined using the syntax:
+## Syntax
 
-```groovy
-name = value
-```
+The Nextflow configuration syntax is based on the Nextflow script syntax. It is designed for setting configuration options in a declarative manner while also allowing for dynamic expressions where appropriate.
 
-Please note, string values need to be wrapped in quotation characters while numbers and boolean values (`true`, `false`) do not. Also note that values are typed. This means that, for example, `1` is different from `'1'` — the former is interpreted as the number one, while the latter is interpreted as a string value.
+A Nextflow config file may consist of any number of *assignments*, *blocks*, and *includes*. Config files may also contain comments in the same manner as scripts.
 
-### Config variables
+See {ref}`syntax-page` for more information about the Nextflow script syntax.
 
-Configuration properties can be used as variables in the configuration file by using the usual `$propertyName` or `${expression}` syntax.
+### Assignments
 
-For example:
+A config assignment consists of a config option and an expression separated by an equals sign:
 
 ```groovy
-propertyOne = 'world'
-anotherProp = "Hello $propertyOne"
-customPath = "$PATH:/my/app/folder"
+workDir = 'work'
+docker.enabled = true
+process.maxErrors = 10
 ```
 
-Please note, the usual rules for {ref}`string-interpolation` are applied, thus a string containing a variable reference must be wrapped in double-quote chars instead of single-quote chars.
-
-The same mechanism allows you to access environment variables defined in the hosting system. Any variable name not defined in the Nextflow configuration file(s) is interpreted to be a reference to an environment variable with that name. So, in the above example, the property `customPath` is defined as the current system `PATH` to which the string `/my/app/folder` is appended.
+A config option consists of an *option name* prefixed by any number of *scopes* separated by dots. Config scopes are used to group related config options. See {ref}`config-options` for the full set of config options.
 
-### Config comments
-
-Configuration files use the same conventions for comments used by the Groovy or Java programming languages. Thus, use `//` to comment a single line, or `/*` .. `*/` to comment a block on multiple lines.
-
-### Config include
-
-A configuration file can include one or more configuration files using the keyword `includeConfig`. For example:
+The expression is typically a literal value such as a number, boolean, or string. However, any expression can be used:
 
 ```groovy
-process.executor = 'sge'
-process.queue = 'long'
-process.memory = '10G'
-
-includeConfig 'path/foo.config'
+params.helper_file = "${projectDir}/assets/helper.txt"
 ```
 
-When a relative path is used, it is resolved against the actual location of the including file.
+### Blocks
 
-## Config scopes
-
-Configuration settings can be organized in different scopes by dot prefixing the property names with a scope identifier, or grouping the properties in the same scope using the curly brackets notation. For example:
+A config scope can also be specified as a block, which may contain multiple configuration options. For example:
 
 ```groovy
-alpha.x = 1
-alpha.y = 'string value..'
-
-beta {
-     p = 2
-     q = 'another string ..'
-}
-```
-
-(config-apptainer)=
-
-### Scope `apptainer`
-
-The `apptainer` scope controls how [Apptainer](https://apptainer.org) containers are executed by Nextflow.
-
-The following settings are available:
-
-`apptainer.autoMounts`
-: When `true` Nextflow automatically mounts host paths in the executed container. It requires the `user bind control` feature to be enabled in your Apptainer installation (default: `true`).
-
-`apptainer.cacheDir`
-: The directory where remote Apptainer images are stored. When using a computing cluster it must be a shared folder accessible to all compute nodes.
-
-`apptainer.enabled`
-: Enable Apptainer execution (default: `false`).
-
-`apptainer.engineOptions`
-: This attribute can be used to provide any option supported by the Apptainer engine i.e. `apptainer [OPTIONS]`.
-
-`apptainer.envWhitelist`
-: Comma separated list of environment variable names to be included in the container environment.
-
-`apptainer.noHttps`
-: Pull the Apptainer image with http protocol (default: `false`).
-
-`apptainer.ociAutoPull`
-: :::{versionadded} 23.12.0-edge
-  :::
-: When enabled, OCI (and Docker) container images are pulled and converted to the SIF format by the Apptainer run command, instead of Nextflow (default: `false`).
-
-  :::{note}
-  Leave `ociAutoPull` disabled if you are willing to build a Singularity/Apptainer native image with Wave (see the {ref}`wave-singularity` section).
-  :::
-
-`apptainer.pullTimeout`
-: The amount of time the Apptainer pull can last, exceeding which the process is terminated (default: `20 min`).
+// dot syntax
+docker.enabled = true
+docker.runOptions = '-u $(id -u):$(id -g)'
 
-`apptainer.registry`
-: The registry from where Docker images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
-
-`apptainer.runOptions`
-: This attribute can be used to provide any extra command line options supported by `apptainer exec`.
-
-Read the {ref}`container-apptainer` page to learn more about how to use Apptainer containers with Nextflow.
-
-(config-aws)=
-
-### Scope `aws`
-
-The `aws` scope controls the interactions with AWS, including AWS Batch and S3. For example:
-
-```groovy
-aws {
-    accessKey = '<YOUR S3 ACCESS KEY>'
-    secretKey = '<YOUR S3 SECRET KEY>'
-    region = 'us-east-1'
-
-    client {
-        maxConnections = 20
-        connectionTimeout = 10000
-        uploadStorageClass = 'INTELLIGENT_TIERING'
-        storageEncryption = 'AES256'
-    }
-    batch {
-        cliPath = '/home/ec2-user/miniconda/bin/aws'
-        maxTransferAttempts = 3
-        delayBetweenAttempts = '5 sec'
-    }
+// block syntax
+docker {
+    enabled = true
+    runOptions = '-u $(id -u):$(id -g)'
 }
 ```
 
-:::{tip}
-This scope can also be used to configure access to S3-compatible storage outside of AWS, such as [Ceph](https://ceph.com/en/) and [MinIO](https://min.io/).
-:::
-
-Read the {ref}`aws-page` and {ref}`amazons3-page` pages for more information.
-
-The following settings are available:
-
-`aws.accessKey`
-: AWS account access key
-
-`aws.profile`
-: :::{versionadded} 22.12.0-edge
-  :::
-: AWS profile from `~/.aws/credentials`
-
-`aws.region`
-: AWS region (e.g. `us-east-1`)
-
-`aws.secretKey`
-: AWS account secret key
-
-`aws.batch.cliPath`
-: The path where the AWS command line tool is installed in the host AMI.
-
-`aws.batch.delayBetweenAttempts`
-: Delay between download attempts from S3 (default: `10 sec`).
-
-`aws.batch.executionRole`
-: :::{versionadded} 23.12.0-edge
-  :::
-: The AWS Batch Execution Role ARN that needs to be used to execute the Batch Job. This is mandatory when using AWS Fargate platform type. See [AWS documentation](https://docs.aws.amazon.com/batch/latest/userguide/execution-IAM-role.html) for more details.
-
-`aws.batch.jobRole`
-: The AWS Batch Job Role ARN that needs to be used to execute the Batch Job.
-
-`aws.batch.logsGroup`
-: :::{versionadded} 22.09.0-edge
-  :::
-: The name of the logs group used by Batch Jobs (default: `/aws/batch/job`).
-
-`aws.batch.maxParallelTransfers`
-: Max parallel upload/download transfer operations *per job* (default: `4`).
-
-`aws.batch.maxSpotAttempts`
-: :::{versionadded} 22.04.0
-  :::
-: Max number of execution attempts of a job interrupted by a EC2 spot reclaim event (default: `5`)
-
-`aws.batch.maxTransferAttempts`
-: Max number of downloads attempts from S3 (default: `1`).
-
-`aws.batch.platformType`
-: :::{versionadded} 23.12.0-edge
-  :::
-: Allow specifying the compute platform type used by AWS Batch, that can be either `ec2` or `fargate`. See AWS documentation to learn more about [AWS Fargate platform type](https://docs.aws.amazon.com/batch/latest/userguide/fargate.html) for AWS Batch.
-
-`aws.batch.retryMode`
-: The retry mode configuration setting, to accommodate rate-limiting on [AWS services](https://docs.aws.amazon.com/cli/latest/userguide/cli-configure-retries.html) (default: `standard`, other options: `legacy`, `adaptive`); this handling is delegated to AWS. To have Nextflow handle retries instead, use `built-in`.
-
-`aws.batch.schedulingPriority`
-: :::{versionadded} 23.01.0-edge
-  :::
-: The scheduling priority for all tasks when using [fair-share scheduling for AWS Batch](https://aws.amazon.com/blogs/hpc/introducing-fair-share-scheduling-for-aws-batch/) (default: `0`)
-
-`aws.batch.shareIdentifier`
-: :::{versionadded} 22.09.0-edge
-  :::
-: The share identifier for all tasks when using [fair-share scheduling for AWS Batch](https://aws.amazon.com/blogs/hpc/introducing-fair-share-scheduling-for-aws-batch/)
-
-`aws.batch.volumes`
-: One or more container mounts. Mounts can be specified as simple e.g. `/some/path` or canonical format e.g. `/host/path:/mount/path[:ro|rw]`. Multiple mounts can be specified separating them with a comma or using a list object.
-
-`aws.client.anonymous`
-: Allow the access of public S3 buckets without the need to provide AWS credentials. Any service that does not accept unsigned requests will return a service access error.
-
-`aws.client.s3Acl`
-: Allow the setting of predefined bucket permissions, also known as *canned ACL*. Permitted values are `Private`, `PublicRead`, `PublicReadWrite`, `AuthenticatedRead`, `LogDeliveryWrite`, `BucketOwnerRead`, `BucketOwnerFullControl`, and `AwsExecRead`. See [Amazon docs](https://docs.aws.amazon.com/AmazonS3/latest/userguide/acl-overview.html#canned-acl) for details.
-
-`aws.client.connectionTimeout`
-: The amount of time to wait (in milliseconds) when initially establishing a connection before timing out.
-
-`aws.client.endpoint`
-: The AWS S3 API entry point e.g. `https://s3-us-west-1.amazonaws.com`. Note: the endpoint must include the protocol prefix e.g. `https://`.
-
-`aws.client.glacierAutoRetrieval`
-: :::{deprecated} 24.02.0-edge
-  Glacier auto-retrieval is no longer supported. Instead, consider using the AWS CLI to restore any Glacier objects before or at the beginning of your pipeline (i.e. in a Nextflow process).
-  :::
-: Enable auto retrieval of S3 objects with a Glacier storage class (default: `false`).
-
-`aws.client.glacierExpirationDays`
-: :::{deprecated} 24.02.0-edge
-  :::
-: The time, in days, between when an object is restored to the bucket and when it expires (default: `7`).
-
-`aws.client.glacierRetrievalTier`
-: :::{deprecated} 24.02.0-edge
-  :::
-: The retrieval tier to use when restoring objects from Glacier, one of [`Expedited`, `Standard`, `Bulk`].
-
-`aws.client.maxConnections`
-: The maximum number of allowed open HTTP connections.
-
-`aws.client.maxErrorRetry`
-: The maximum number of retry attempts for failed retryable requests.
-
-`aws.client.protocol`
-: The protocol (i.e. HTTP or HTTPS) to use when connecting to AWS.
-
-`aws.client.proxyHost`
-: The proxy host to connect through.
-
-`aws.client.proxyPort`
-: The port on the proxy host to connect through.
-
-`aws.client.proxyUsername`
-: The user name to use when connecting through a proxy.
-
-`aws.client.proxyPassword`
-: The password to use when connecting through a proxy.
-
-`aws.client.requesterPays`
-: :::{versionadded} 24.05.0-edge
-  :::
-: Enable the requester pays feature for S3 buckets.
-
-`aws.client.s3PathStyleAccess`
-: Enable the use of path-based access model that is used to specify the address of an object in S3-compatible storage systems.
-
-`aws.client.signerOverride`
-: The name of the signature algorithm to use for signing requests made by the client.
-
-`aws.client.socketSendBufferSizeHint`
-: The Size hint (in bytes) for the low level TCP send buffer.
-
-`aws.client.socketRecvBufferSizeHint`
-: The Size hint (in bytes) for the low level TCP receive buffer.
-
-`aws.client.socketTimeout`
-: The amount of time to wait (in milliseconds) for data to be transferred over an established, open connection before the connection is timed out.
-
-`aws.client.storageEncryption`
-: The S3 server side encryption to be used when saving objects on S3, either `AES256` or `aws:kms` values are allowed.
-
-`aws.client.storageKmsKeyId`
-: :::{versionadded} 22.05.0-edge
-  :::
-: The AWS KMS key Id to be used to encrypt files stored in the target S3 bucket.
-
-`aws.client.userAgent`
-: The HTTP user agent header passed with all HTTP requests.
-
-`aws.client.uploadChunkSize`
-: The size of a single part in a multipart upload (default: `100 MB`).
-
-`aws.client.uploadMaxAttempts`
-: The maximum number of upload attempts after which a multipart upload returns an error (default: `5`).
-
-`aws.client.uploadMaxThreads`
-: The maximum number of threads used for multipart upload.
-
-`aws.client.uploadRetrySleep`
-: The time to wait after a failed upload attempt to retry the part upload (default: `500ms`).
-
-`aws.client.uploadStorageClass`
-: The S3 storage class applied to stored objects, one of \[`STANDARD`, `STANDARD_IA`, `ONEZONE_IA`, `INTELLIGENT_TIERING`\] (default: `STANDARD`).
-
-(config-azure)=
-
-### Scope `azure`
-
-The `azure` scope allows you to configure the interactions with Azure, including Azure Batch and Azure Blob Storage.
-
-Read the {ref}`azure-page` page for more information.
-
-The following settings are available:
-
-`azure.activeDirectory.servicePrincipalId`
-: The service principal client ID
-
-`azure.activeDirectory.servicePrincipalSecret`
-: The service principal client secret
-
-`azure.activeDirectory.tenantId`
-: The Azure tenant ID
-
-`azure.batch.accountName`
-: The batch service account name.
-
-`azure.batch.accountKey`
-: The batch service account key.
-
-`azure.batch.allowPoolCreation`
-: Enable the automatic creation of batch pools specified in the Nextflow configuration file (default: `false`).
-
-`azure.batch.autoPoolMode`
-: Enable the automatic creation of batch pools depending on the pipeline resources demand (default: `true`).
-
-`azure.batch.copyToolInstallMode`
-: Specify where the `azcopy` tool used by Nextflow. When `node` is specified it's copied once during the pool creation. When `task` is provider, it's installed for each task execution. Finally when `off` is specified, the `azcopy` tool is not installed (default: `node`).
-
-`azure.batch.deleteJobsOnCompletion`
-: Delete all jobs when the workflow completes (default: `false`).
-: :::{versionchanged} 23.08.0-edge
-  Default value was changed from `true` to `false`.
-  :::
-
-`azure.batch.deletePoolsOnCompletion`
-: Delete all compute node pools when the workflow completes (default: `false`).
-
-`azure.batch.deleteTasksOnCompletion`
-: :::{versionadded} 23.08.0-edge
-  :::
-: Delete each task when it completes (default: `true`).
-: Although this setting is enabled by default, failed tasks will not be deleted unless it is explicitly enabled. This way, the default behavior is that successful tasks are deleted while failed tasks are preserved for debugging purposes.
-
-`azure.batch.endpoint`
-: The batch service endpoint e.g. `https://nfbatch1.westeurope.batch.azure.com`.
-
-`azure.batch.location`
-: The name of the batch service region, e.g. `westeurope` or `eastus2`. This is not needed when the endpoint is specified.
-
-`azure.batch.terminateJobsOnCompletion`
-: :::{versionadded} 23.05.0-edge
-  :::
-: When the workflow completes, set all jobs to terminate on task completion. (default: `true`).
-
-`azure.batch.pools.<name>.autoScale`
-: Enable autoscaling feature for the pool identified with `<name>`.
-
-`azure.batch.pools.<name>.fileShareRootPath`
-: If mounting File Shares, this is the internal root mounting point. Must be `/mnt/resource/batch/tasks/fsmounts` for CentOS nodes or `/mnt/batch/tasks/fsmounts` for Ubuntu nodes (default is for CentOS).
-
-`azure.batch.pools.<name>.lowPriority`
-: Enable the use of low-priority VMs (default: `false`).
-
-`azure.batch.pools.<name>.maxVmCount`
-: Specify the max of virtual machine when using auto scale option.
-
-`azure.batch.pools.<name>.mountOptions`
-: Specify the mount options for mounting the file shares (default: `-o vers=3.0,dir_mode=0777,file_mode=0777,sec=ntlmssp`).
-
-`azure.batch.pools.<name>.offer`
-: Specify the offer type of the virtual machine type used by the pool identified with `<name>` (default: `centos-container`).
-
-`azure.batch.pools.<name>.privileged`
-: Enable the task to run with elevated access. Ignored if `runAs` is set (default: `false`).
-
-`azure.batch.pools.<name>.publisher`
-: Specify the publisher of virtual machine type used by the pool identified with `<name>` (default: `microsoft-azure-batch`).
-
-`azure.batch.pools.<name>.runAs`
-: Specify the username under which the task is run. The user must already exist on each node of the pool.
-
-`azure.batch.pools.<name>.scaleFormula`
-: Specify the scale formula for the pool identified with `<name>`. See Azure Batch [scaling documentation](https://docs.microsoft.com/en-us/azure/batch/batch-automatic-scaling) for details.
-
-`azure.batch.pools.<name>.scaleInterval`
-: Specify the interval at which to automatically adjust the Pool size according to the autoscale formula. The minimum and maximum value are 5 minutes and 168 hours respectively (default: `10 mins`).
-
-`azure.batch.pools.<name>.schedulePolicy`
-: Specify the scheduling policy for the pool identified with `<name>`. It can be either `spread` or `pack` (default: `spread`).
-
-`azure.batch.pools.<name>.sku`
-: Specify the ID of the Compute Node agent SKU which the pool identified with `<name>` supports (default: `batch.node.centos 8`).
-
-`azure.batch.pools.<name>.startTask.script`
-: :::{versionadded} 24.03.0-edge
-  :::
-: Specify the `startTask` that is executed as the node joins the Azure Batch node pool.
-
-`azure.batch.pools.<name>.startTask.privileged`
-: :::{versionadded} 24.03.0-edge
-  :::
-: Enable the `startTask` to run with elevated access (default: `false`).
-
-`azure.batch.pools.<name>.virtualNetwork`
-: :::{versionadded} 23.03.0-edge
-  :::
-: Specify the subnet ID of a virtual network in which to create the pool.
-
-`azure.batch.pools.<name>.vmCount`
-: Specify the number of virtual machines provisioned by the pool identified with `<name>`.
-
-`azure.batch.pools.<name>.vmType`
-: Specify the virtual machine type used by the pool identified with `<name>`.
-
-`azure.managedIdentity.clientId`
-: Specify the client ID for an Azure [managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/overview). See {ref}`azure-managed-identities` for more details.
-
-`azure.managedIdentity.system`
-: When `true`, use the system-assigned [managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/overview) to authenticate Azure resources. See {ref}`azure-managed-identities` for more details.
-
-`azure.managedIdentity.tenantId`
-: The Azure tenant ID
-
-`azure.registry.server`
-: Specify the container registry from which to pull the Docker images (default: `docker.io`).
-
-`azure.registry.userName`
-: Specify the username to connect to a private container registry.
-
-`azure.registry.password`
-: Specify the password to connect to a private container registry.
-
-`azure.retryPolicy.delay`
-: Delay when retrying failed API requests (default: `500ms`).
-
-`azure.retryPolicy.jitter`
-: Jitter value when retrying failed API requests (default: `0.25`).
-
-`azure.retryPolicy.maxAttempts`
-: Max attempts when retrying failed API requests (default: `10`).
-
-`azure.retryPolicy.maxDelay`
-: Max delay when retrying failed API requests (default: `90s`).
-
-`azure.storage.accountName`
-: The blob storage account name
-
-`azure.storage.accountKey`
-: The blob storage account key
-
-`azure.storage.sasToken`
-: The blob storage shared access signature token. This can be provided as an alternative to the `accountKey` setting.
-
-`azure.storage.tokenDuration`
-: The duration of the shared access signature token created by Nextflow when the `sasToken` option is *not* specified (default: `48h`).
-
-(config-charliecloud)=
-
-### Scope `charliecloud`
-
-The `charliecloud` scope controls how [Charliecloud](https://hpc.github.io/charliecloud/) containers are executed by Nextflow.
-If `charliecloud.writeFake` is unset / `false`, charliecloud will create a copy of the container in the process working directory.
-
-The following settings are available:
-
-`charliecloud.cacheDir`
-: The directory where remote Charliecloud images are stored. When using a computing cluster it must be a shared folder accessible to all compute nodes.
-
-`charliecloud.enabled`
-: Enable Charliecloud execution (default: `false`).
-
-`charliecloud.envWhitelist`
-: Comma separated list of environment variable names to be included in the container environment.
-
-`charliecloud.pullTimeout`
-: The amount of time the Charliecloud pull can last, exceeding which the process is terminated (default: `20 min`).
-
-`charliecloud.runOptions`
-: This attribute can be used to provide any extra command line options supported by the `ch-run` command.
-
-`charliecloud.temp`
-: Mounts a path of your choice as the `/tmp` directory in the container. Use the special value `auto` to create a temporary directory each time a container is created.
-
-`charliecloud.registry`
-: The registry from where images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
-
-`charliecloud.writeFake`
-: Enable `writeFake` with charliecloud. This allows to run containers from storage in writeable mode, using overlayfs, see [charliecloud documentation](https://hpc.github.io/charliecloud/ch-run.html#ch-run-overlay) for details 
-
-`charliecloud.useSquash`
-: Create a temporary squashFS container image in the process work directory instead of a folder.
-
-Read the {ref}`container-charliecloud` page to learn more about how to use Charliecloud containers with Nextflow.
-
-(config-conda)=
-
-### Scope `conda`
-
-The `conda` scope controls the creation of a Conda environment by the Conda package manager.
-
-The following settings are available:
-
-`conda.enabled`
-: Enable Conda execution (default: `false`).
-
-`conda.cacheDir`
-: Defines the path where Conda environments are stored. When using a compute cluster make sure to provide a shared file system path accessible from all compute nodes.
-
-`conda.createOptions`
-: Defines any extra command line options supported by the `conda create` command. For details see the [Conda documentation](https://docs.conda.io/projects/conda/en/latest/commands/create.html).
-
-`conda.createTimeout`
-: Defines the amount of time the Conda environment creation can last. The creation process is terminated when the timeout is exceeded (default: `20 min`).
-
-`conda.useMamba`
-: Uses the `mamba` binary instead of `conda` to create the Conda environments. For details see the [Mamba documentation](https://github.com/mamba-org/mamba).
-
-`conda.useMicromamba`
-: :::{versionadded} 22.05.0-edge
-  :::
-: uses the `micromamba` binary instead of `conda` to create the Conda environments. For details see the [Micromamba documentation](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html).
-
-Read the {ref}`conda-page` page to learn more about how to use Conda environments with Nextflow.
-
-(config-dag)=
-
-### Scope `dag`
-
-The `dag` scope controls the workflow diagram generated by Nextflow.
-
-The following settings are available:
-
-`dag.enabled`
-: When `true` enables the generation of the DAG file (default: `false`).
-
-`dag.depth`
-: :::{versionadded} 23.10.0
-  :::
-: *Only supported by the HTML and Mermaid renderers.*
-: Controls the maximum depth at which to render sub-workflows (default: no limit).
-
-`dag.direction`
-: :::{versionadded} 23.10.0
-  :::
-: *Only supported by the HTML and Mermaid renderers.*
-: Controls the direction of the DAG, can be `'LR'` (left-to-right) or `'TB'` (top-to-bottom) (default: `'TB'`).
-
-`dag.file`
-: Graph file name (default: `dag-<timestamp>.html`).
-
-`dag.overwrite`
-: When `true` overwrites any existing DAG file with the same name (default: `false`).
-
-`dag.verbose`
-: :::{versionadded} 23.10.0
-  :::
-: *Only supported by the HTML and Mermaid renderers.*
-: When `false`, channel names are omitted, operators are collapsed, and empty workflow inputs are removed (default: `false`).
-
-Read the {ref}`dag-visualisation` page to learn more about the workflow graph that can be generated by Nextflow.
-
-(config-docker)=
-
-### Scope `docker`
-
-The `docker` scope controls how [Docker](https://www.docker.com) containers are executed by Nextflow.
-
-The following settings are available:
-
-`docker.enabled`
-: Enable Docker execution (default: `false`).
-
-`docker.engineOptions`
-: This attribute can be used to provide any option supported by the Docker engine i.e. `docker [OPTIONS]`.
-
-`docker.envWhitelist`
-: Comma separated list of environment variable names to be included in the container environment.
-
-`docker.fixOwnership`
-: Fix ownership of files created by the docker container.
-
-`docker.legacy`
-: Use command line options removed since Docker 1.10.0 (default: `false`).
-
-`docker.mountFlags`
-: Add the specified flags to the volume mounts e.g. `mountFlags = 'ro,Z'`.
-
-`docker.registry`
-: The registry from where Docker images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
-
-`docker.remove`
-: Clean-up the container after the execution (default: `true`). See the [Docker documentation](https://docs.docker.com/engine/reference/run/#clean-up---rm) for details.
-
-`docker.runOptions`
-: This attribute can be used to provide any extra command line options supported by the `docker run` command. See the [Docker documentation](https://docs.docker.com/engine/reference/run/) for details.
-
-`docker.sudo`
-: Executes Docker run command as `sudo` (default: `false`).
-
-`docker.temp`
-: Mounts a path of your choice as the `/tmp` directory in the container. Use the special value `auto` to create a temporary directory each time a container is created.
-
-`docker.tty`
-: Allocates a pseudo-tty (default: `false`).
-
-Read the {ref}`container-docker` page to learn more about how to use Docker containers with Nextflow.
-
-(config-env)=
-
-### Scope `env`
-
-The `env` scope allows the definition one or more variables that will be exported into the environment where workflow tasks are executed.
-
-Simply prefix your variable names with the `env` scope or surround them by curly brackets, as shown below:
+As a result, deeply nested config options can be assigned in various ways. For example, the following three assignments are equivalent:
 
 ```groovy
-env.ALPHA = 'some value'
-env.BETA = "$HOME/some/path"
-
-env {
-     DELTA = 'one more'
-     GAMMA = "/my/path:$PATH"
-}
-```
-
-:::{note}
-In the above example, variables like `$HOME` and `$PATH` are evaluated when the workflow is launched. If you want these variables to be evaluated during task execution, escape them with `\$`. This difference is important for variables like `$PATH`, which may be different in the workflow environment versus the task environment.
-:::
-
-:::{warning}
-The `env` scope provides environment variables to *tasks*, not Nextflow itself. Nextflow environment variables such as `NXF_VER` should be set in the environment in which Nextflow is launched.
-:::
-
-(config-executor)=
-
-### Scope `executor`
-
-The `executor` scope controls various executor behaviors.
-
-The following settings are available:
-
-`executor.account`
-: :::{versionadded} 24.04.0
-  :::
-: *Used only by the {ref}`slurm-executor`, {ref}`lsf-executor`, {ref}`pbs-executor` and {ref}`pbspro-executor` executors.*
-: Allows specifying the project or organisation account that should be charged for running the pipeline jobs.
-
-`executor.cpus`
-: The maximum number of CPUs made available by the underlying system. Used only by the `local` executor.
+executor.retry.maxAttempt = 5
 
-`executor.dumpInterval`
-: Determines how often to log the executor status (default: `5min`).
-
-`executor.exitReadTimeout`
-: Determines how long to wait before returning an error status when a process is terminated but the `.exitcode` file does not exist or is empty (default: `270 sec`). Used only by grid executors.
-
-`executor.jobName`
-: Determines the name of jobs submitted to the underlying cluster executor e.g. `executor.jobName = { "$task.name - $task.hash" }`. Make sure the resulting job name matches the validation constraints of the underlying batch scheduler. This setting is only support by the following executors: Bridge, Condor, Flux, HyperQueue, Lsf, Moab, Nqsii, Oar, Pbs, PbsPro, Sge, Slurm and Google Batch.
-
-`executor.killBatchSize`
-: Determines the number of jobs that can be killed in a single command execution (default: `100`).
-
-`executor.memory`
-: The maximum amount of memory made available by the underlying system. Used only by the `local` executor.
-
-`executor.name`
-: The name of the executor to be used (default: `local`).
-
-`executor.perCpuMemAllocation`
-: :::{versionadded} 23.07.0-edge
-  :::
-: *Used only by the {ref}`slurm-executor` executor.*
-: When `true`, specifies memory allocations for SLURM jobs as `--mem-per-cpu <task.memory / task.cpus>` instead of `--mem <task.memory>`.
-
-`executor.perJobMemLimit`
-: Specifies Platform LSF *per-job* memory limit mode. See {ref}`lsf-executor`.
-
-`executor.perTaskReserve`
-: Specifies Platform LSF *per-task* memory reserve mode. See {ref}`lsf-executor`.
-
-`executor.pollInterval`
-: Determines how often to check for process termination. Default varies for each executor (see below).
-
-`executor.queueGlobalStatus`
-: :::{versionadded} 23.01.0-edge
-  :::
-: Determines how job status is retrieved. When `false` only the queue associated with the job execution is queried. When `true` the job status is queried globally i.e. irrespective of the submission queue (default: `false`).
-
-`executor.queueSize`
-: The number of tasks the executor will handle in a parallel manner. A queue size of zero corresponds to no limit. Default varies for each executor (see below).
-
-`executor.queueStatInterval`
-: Determines how often to fetch the queue status from the scheduler (default: `1min`). Used only by grid executors.
-
-`executor.retry.delay`
-: :::{versionadded} 22.03.0-edge
-  :::
-: Delay when retrying failed job submissions (default: `500ms`). Used only by grid executors.
-
-`executor.retry.jitter`
-: :::{versionadded} 22.03.0-edge
-  :::
-: Jitter value when retrying failed job submissions (default: `0.25`). Used only by grid executors.
-
-`executor.retry.maxAttempt`
-: :::{versionadded} 22.03.0-edge
-  :::
-: Max attempts when retrying failed job submissions (default: `3`). Used only by grid executors.
-
-`executor.retry.maxDelay`
-: :::{versionadded} 22.03.0-edge
-  :::
-: Max delay when retrying failed job submissions (default: `30s`). Used only by grid executors.
-
-`executor.retry.reason`
-: :::{versionadded} 22.03.0-edge
-  :::
-: Regex pattern that when verified cause a failed submit operation to be re-tried (default: `Socket timed out`). Used only by grid executors.
-
-`executor.submitRateLimit`
-: Determines the max rate of job submission per time unit, for example `'10sec'` (10 jobs per second) or `'50/2min'` (50 jobs every 2 minutes) (default: unlimited).
-
-Some executor settings have different default values depending on the executor.
-
-| Executor       | `queueSize` | `pollInterval` |
-| -------------- | ----------- | -------------- |
-| AWS Batch      | `1000`      | `10s`          |
-| Azure Batch    | `1000`      | `10s`          |
-| Google Batch   | `1000`      | `10s`          |
-| Grid Executors | `100`       | `5s`           |
-| Kubernetes     | `100`       | `5s`           |
-| Local          | N/A         | `100ms`        |
-
-The executor settings can be defined as shown below:
-
-```groovy
 executor {
-    name = 'sge'
-    queueSize = 200
-    pollInterval = '30 sec'
+    retry.maxAttempt = 5
 }
-```
 
-When using two (or more) different executors in your pipeline, you can specify their settings separately by prefixing the executor name with the symbol `$` and using it as special scope identifier. For example:
-
-```groovy
 executor {
-  $sge {
-      queueSize = 100
-      pollInterval = '30sec'
-  }
-
-  $local {
-      cpus = 8
-      memory = '32 GB'
-  }
+    retry {
+        maxAttempt = 5
+    }
 }
 ```
 
-The above configuration example can be rewritten using the dot notation as shown below:
-
-```groovy
-executor.$sge.queueSize = 100
-executor.$sge.pollInterval = '30sec'
-executor.$local.cpus = 8
-executor.$local.memory = '32 GB'
-```
-
-(config-fusion)=
-
-### Scope `fusion`
-
-The `fusion` scope provides advanced configuration for the use of the {ref}`Fusion file system <fusion-page>`.
-
-The following settings are available:
-
-`fusion.enabled`
-: Enable/disable the use of Fusion file system.
-
-`fusion.cacheSize`
-: :::{versionadded} 23.11.0-edge
-  :::
-: The maximum size of the local cache used by the Fusion client.
-
-`fusion.containerConfigUrl`
-: The URL from where the container layer provisioning the Fusion client is downloaded.
-
-`fusion.exportStorageCredentials`
-: :::{versionadded} 23.05.0-edge
-  This option was previously named `fusion.exportAwsAccessKeys`.
-  :::
-: When `true` the access credentials required by the underlying object storage are exported to the task execution environment.
-
-`fusion.logLevel`
-: The level of logging emitted by the Fusion client.
-
-`fusion.logOutput`
-: Where the logging output is written. 
-
-`fusion.privileged`
-: :::{versionadded} 23.10.0
-  :::
-: Enables the use of privileged containers when using Fusion (default: `true`).
-: The use of Fusion without privileged containers is currently only supported for Kubernetes, and it requires the [k8s-fuse-plugin](https://github.com/nextflow-io/k8s-fuse-plugin) (or similar FUSE device plugin) to be installed in the cluster.
-
-`fusion.tags`
-: The pattern that determines how tags are applied to files created via the Fusion client (default: `[.command.*|.exitcode|.fusion.*](nextflow.io/metadata=true),[*](nextflow.io/temporary=true)`).
-: To disable tags set it to `false`.
-
-(config-google)=
-
-### Scope `google`
-
-The `google` scope allows you to configure the interactions with Google Cloud, including Google Cloud Batch, Google Life Sciences, and Google Cloud Storage.
-
-Read the {ref}`google-page` page for more information.
-
-#### Cloud Batch
-
-The following settings are available for Google Cloud Batch:
-
-`google.batch.autoRetryExitCodes`
-: :::{versionadded} 24.07.0-edge
-  :::
-: Defines the list of exit codes that will be automatically retried by Google Batch when `google.batch.maxSpotAttempts` is greater than 0 (default `[50001]`). Refer to the [Google Batch documentation](https://cloud.google.com/batch/docs/troubleshooting#reserved-exit-codes) for the list of retryable exit codes.
-
-`google.enableRequesterPaysBuckets`
-: When `true` uses the given Google Cloud project ID as the billing project for storage access. This is required when accessing data from *requester pays enabled* buckets. See [Requester Pays on Google Cloud Storage documentation](https://cloud.google.com/storage/docs/requester-pays) (default: `false`).
-
-`google.httpConnectTimeout`
-: :::{versionadded} 23.06.0-edge
-  :::
-: Defines the HTTP connection timeout for Cloud Storage API requests (default: `'60s'`).
-
-`google.httpReadTimeout`
-: :::{versionadded} 23.06.0-edge
-  :::
-: Defines the HTTP read timeout for Cloud Storage API requests (default: `'60s'`).
-
-`google.location`
-: The Google Cloud location where jobs are executed (default: `us-central1`).
-
-`google.batch.maxSpotAttempts`
-: :::{versionadded} 23.11.0-edge
-  :::
-: Max number of execution attempts of a job interrupted by a Compute Engine spot reclaim event (default: `5`).
-: See also: `google.batch.autoRetryExitCodes`
-
-`google.project`
-: The Google Cloud project ID to use for pipeline execution
-
-`google.batch.allowedLocations`
-: :::{versionadded} 22.12.0-edge
-  :::
-: Define the set of allowed locations for VMs to be provisioned. See [Google documentation](https://cloud.google.com/batch/docs/reference/rest/v1/projects.locations.jobs#locationpolicy) for details (default: no restriction).
-
-`google.batch.bootDiskSize`
-: Set the size of the virtual machine boot disk, e.g `50.GB` (default: none).
-
-`google.batch.cpuPlatform`
-: Set the minimum CPU Platform, e.g. `'Intel Skylake'`. See [Specifying a minimum CPU Platform for VM instances](https://cloud.google.com/compute/docs/instances/specify-min-cpu-platform#specifications) (default: none).
-
-`google.batch.network`
-: The URL of an existing network resource to which the VM will be attached.
-
-  You can specify the network as a full or partial URL. For example, the following are all valid URLs:
-
-  - https://www.googleapis.com/compute/v1/projects/{project}/global/networks/{network}
-  - projects/{project}/global/networks/{network}
-  - global/networks/{network}
-
-`google.batch.serviceAccountEmail`
-: Define the Google service account email to use for the pipeline execution. If not specified, the default Compute Engine service account for the project will be used.
-
-  Note that the `google.batch.serviceAccountEmail` service account will only be used for spawned jobs, not for the Nextflow process itself. 
-  See the [Google Cloud](https://www.nextflow.io/docs/latest/google.html#credentials) documentation for more information on credentials.
-
-`google.batch.spot`
-: When `true` enables the usage of *spot* virtual machines or `false` otherwise (default: `false`).
-
-`google.batch.subnetwork`
-: The URL of an existing subnetwork resource in the network to which the VM will be attached.
-
-  You can specify the subnetwork as a full or partial URL. For example, the following are all valid URLs:
-
-  - https://www.googleapis.com/compute/v1/projects/{project}/regions/{region}/subnetworks/{subnetwork}
-  - projects/{project}/regions/{region}/subnetworks/{subnetwork}
-  - regions/{region}/subnetworks/{subnetwork}
-
-`google.batch.usePrivateAddress`
-: When `true` the VM will NOT be provided with a public IP address, and only contain an internal IP. If this option is enabled, the associated job can only load docker images from Google Container Registry, and the job executable cannot use external services other than Google APIs (default: `false`).
-
-`google.storage.maxAttempts`
-: :::{versionadded} 23.11.0-edge
-  :::
-: Max attempts when retrying failed API requests to Cloud Storage (default: `10`).
-
-`google.storage.maxDelay`
-: :::{versionadded} 23.11.0-edge
-  :::
-: Max delay when retrying failed API requests to Cloud Storage (default: `'90s'`).
-
-`google.storage.multiplier`
-: :::{versionadded} 23.11.0-edge
-  :::
-: Delay multiplier when retrying failed API requests to Cloud Storage (default: `2.0`).
-
-#### Cloud Life Sciences
-
-The following settings are available for Cloud Life Sciences:
-
-`google.enableRequesterPaysBuckets`
-: When `true` uses the given Google Cloud project ID as the billing project for storage access. This is required when accessing data from *requester pays enabled* buckets. See [Requester Pays on Google Cloud Storage documentation](https://cloud.google.com/storage/docs/requester-pays) (default: `false`).
-
-`google.httpConnectTimeout`
-: :::{versionadded} 23.06.0-edge
-  :::
-: Defines the HTTP connection timeout for Cloud Storage API requests (default: `'60s'`).
-
-`google.httpReadTimeout`
-: :::{versionadded} 23.06.0-edge
-  :::
-: Defines the HTTP read timeout for Cloud Storage API requests (default: `'60s'`).
-
-`google.location`
-: The Google Cloud location where jobs are executed (default: `us-central1`).
-
-`google.project`
-: The Google Cloud project ID to use for pipeline execution
-
-`google.region`
-: The Google Cloud region where jobs are executed. Multiple regions can be provided as a comma-separated list. Cannot be used with the `google.zone` option. See the [Google Cloud documentation](https://cloud.google.com/compute/docs/regions-zones/) for a list of available regions and zones.
-
-`google.zone`
-: The Google Cloud zone where jobs are executed. Multiple zones can be provided as a comma-separated list. Cannot be used with the `google.region` option. See the [Google Cloud documentation](https://cloud.google.com/compute/docs/regions-zones/) for a list of available regions and zones.
-
-`google.batch.allowedLocations`
-: :::{versionadded} 22.12.0-edge
-  :::
-: Define the set of allowed locations for VMs to be provisioned. See [Google documentation](https://cloud.google.com/batch/docs/reference/rest/v1/projects.locations.jobs#locationpolicy) for details (default: no restriction).
-
-`google.batch.bootDiskSize`
-: Set the size of the virtual machine boot disk, e.g `50.GB` (default: none).
-
-`google.batch.cpuPlatform`
-: Set the minimum CPU Platform, e.g. `'Intel Skylake'`. See [Specifying a minimum CPU Platform for VM instances](https://cloud.google.com/compute/docs/instances/specify-min-cpu-platform#specifications) (default: none).
-
-`google.batch.installGpuDrivers`
-: :::{versionadded} 23.08.0-edge
-  :::
-: When `true` automatically installs the appropriate GPU drivers to the VM when a GPU is requested (default: `false`). Only needed when using an instance template.
-
-`google.batch.network`
-: Set network name to attach the VM's network interface to. The value will be prefixed with `global/networks/` unless it contains a `/`, in which case it is assumed to be a fully specified network resource URL. If unspecified, the global default network is used.
-
-`google.batch.serviceAccountEmail`
-: Define the Google service account email to use for the pipeline execution. If not specified, the default Compute Engine service account for the project will be used.
-
-`google.batch.spot`
-: When `true` enables the usage of *spot* virtual machines or `false` otherwise (default: `false`).
-
-`google.batch.subnetwork`
-: Define the name of the subnetwork to attach the instance to must be specified here, when the specified network is configured for custom subnet creation. The value is prefixed with `regions/subnetworks/` unless it contains a `/`, in which case it is assumed to be a fully specified subnetwork resource URL.
-
-`google.batch.usePrivateAddress`
-: When `true` the VM will NOT be provided with a public IP address, and only contain an internal IP. If this option is enabled, the associated job can only load docker images from Google Container Registry, and the job executable cannot use external services other than Google APIs (default: `false`).
-
-`google.lifeSciences.bootDiskSize`
-: Set the size of the virtual machine boot disk e.g `50.GB` (default: none).
-
-`google.lifeSciences.copyImage`
-: The container image run to copy input and output files. It must include the `gsutil` tool (default: `google/cloud-sdk:alpine`).
-
-`google.lifeSciences.cpuPlatform`
-: Set the minimum CPU Platform e.g. `'Intel Skylake'`. See [Specifying a minimum CPU Platform for VM instances](https://cloud.google.com/compute/docs/instances/specify-min-cpu-platform#specifications) (default: none).
-
-`google.lifeSciences.debug`
-: When `true` copies the `/google` debug directory in that task bucket directory (default: `false`).
-
-`google.lifeSciences.keepAliveOnFailure`
-: :::{versionadded} 21.06.0-edge
-  :::
-: When `true` and a task complete with an unexpected exit status the associated compute node is kept up for 1 hour. This options implies `sshDaemon=true` (default: `false`).
-
-`google.lifeSciences.network`
-: :::{versionadded} 21.03.0-edge
-  :::
-: Set network name to attach the VM's network interface to. The value will be prefixed with `global/networks/` unless it contains a `/`, in which case it is assumed to be a fully specified network resource URL. If unspecified, the global default network is used.
-
-`google.lifeSciences.preemptible`
-: When `true` enables the usage of *preemptible* virtual machines or `false` otherwise (default: `true`).
-
-`google.lifeSciences.serviceAccountEmail`
-: :::{versionadded} 20.05.0-edge
-  :::
-: Define the Google service account email to use for the pipeline execution. If not specified, the default Compute Engine service account for the project will be used.
-
-`google.lifeSciences.subnetwork`
-: :::{versionadded} 21.03.0-edge
-  :::
-: Define the name of the subnetwork to attach the instance to must be specified here, when the specified network is configured for custom subnet creation. The value is prefixed with `regions/subnetworks/` unless it contains a `/`, in which case it is assumed to be a fully specified subnetwork resource URL.
-
-`google.lifeSciences.sshDaemon`
-: When `true` runs SSH daemon in the VM carrying out the job to which it's possible to connect for debugging purposes (default: `false`).
+### Includes
 
-`google.lifeSciences.sshImage`
-: The container image used to run the SSH daemon (default: `gcr.io/cloud-genomics-pipelines/tools`).
-
-`google.lifeSciences.usePrivateAddress`
-: :::{versionadded} 20.03.0-edge
-  :::
-: When `true` the VM will NOT be provided with a public IP address, and only contain an internal IP. If this option is enabled, the associated job can only load docker images from Google Container Registry, and the job executable cannot use external services other than Google APIs (default: `false`).
-
-`google.storage.delayBetweenAttempts`
-: :::{versionadded} 21.06.0-edge
-  :::
-: Delay between download attempts from Google Storage (default `10 sec`).
-
-`google.storage.downloadMaxComponents`
-: :::{versionadded} 21.06.0-edge
-  :::
-: Defines the value for the option `GSUtil:sliced_object_download_max_components` used by `gsutil` for transfer input and output data (default: `8`).
-
-`google.storage.maxParallelTransfers`
-: :::{versionadded} 21.06.0-edge
-  :::
-: Max parallel upload/download transfer operations *per job* (default: `4`).
-
-`google.storage.maxTransferAttempts`
-: :::{versionadded} 21.06.0-edge
-  :::
-: Max number of downloads attempts from Google Storage (default: `1`).
-
-`google.storage.parallelThreadCount`
-: :::{versionadded} 21.06.0-edge
-  :::
-: Defines the value for the option `GSUtil:parallel_thread_count` used by `gsutil` for transfer input and output data (default: `1`).
-
-(config-k8s)=
-
-### Scope `k8s`
-
-The `k8s` scope controls the deployment and execution of workflow applications in a Kubernetes cluster.
-
-The following settings are available:
-
-`k8s.autoMountHostPaths`
-: Automatically mounts host paths into the task pods (default: `false`). Only intended for development purposes when using a single node.
-
-`k8s.computeResourceType`
-: :::{versionadded} 22.05.0-edge
-  :::
-: Define whether use Kubernetes `Pod` or `Job` resource type to carry out Nextflow tasks (default: `Pod`).
-
-`k8s.context`
-: Defines the Kubernetes [configuration context name](https://kubernetes.io/docs/tasks/access-application-cluster/configure-access-multiple-clusters/) to use.
-
-`k8s.cpuLimits`
-: :::{versionadded} 24.04.0
-  :::
-: When `true`, set both the pod CPUs `request` and `limit` to the value specified by the `cpus` directive, otherwise set only the `request` (default: `false`).
-: This setting is useful when a K8s cluster requires a CPU limit to be defined through a [LimitRange](https://kubernetes.io/docs/concepts/policy/limit-range/).
-
-`k8s.debug.yaml`
-: When `true`, saves the pod spec for each task to `.command.yaml` in the task directory (default: `false`).
-
-`k8s.fetchNodeName`
-: :::{versionadded} 22.05.0-edge
-  :::
-: If you trace the hostname, activate this option (default: `false`).
-
-`k8s.fuseDevicePlugin`
-: :::{versionadded} 24.01.0-edge
-  :::
-: The FUSE device plugin to be used when enabling Fusion in unprivileged mode (default: `['nextflow.io/fuse': 1]`).
-
-`k8s.httpConnectTimeout`
-: :::{versionadded} 22.10.0
-  :::
-: Defines the Kubernetes client request HTTP connection timeout e.g. `'60s'`.
-
-`k8s.httpReadTimeout`
-: :::{versionadded} 22.10.0
-  :::
-: Defines the Kubernetes client request HTTP connection read timeout e.g. `'60s'`.
-
-`k8s.launchDir`
-: Defines the path where the workflow is launched and the user data is stored. This must be a path in a shared K8s persistent volume (default: `<volume-claim-mount-path>/<user-name>`).
-
-`k8s.maxErrorRetry`
-: :::{versionadded} 22.09.6-edge
-  :::
-: Defines the Kubernetes API max request retries (default: 4).
-
-`k8s.namespace`
-: Defines the Kubernetes namespace to use (default: `default`).
-
-`k8s.pod`
-: Allows the definition of one or more pod configuration options such as environment variables, config maps, secrets, etc. It allows the same settings as the {ref}`process-pod` process directive.
-: When using the `kuberun` command, this setting also applies to the submitter pod.
-
-`k8s.projectDir`
-: Defines the path where Nextflow projects are downloaded. This must be a path in a shared K8s persistent volume (default: `<volume-claim-mount-path>/projects`).
-
-`k8s.pullPolicy`
-: Defines the strategy to be used to pull the container image e.g. `pullPolicy: 'Always'`.
-
-`k8s.runAsUser`
-: Defines the user ID to be used to run the containers. Shortcut for the `securityContext` option.
-
-`k8s.securityContext`
-: Defines the [security context](https://kubernetes.io/docs/tasks/configure-pod-container/security-context/) for all pods.
-
-`k8s.serviceAccount`
-: Defines the Kubernetes [service account name](https://kubernetes.io/docs/tasks/configure-pod-container/configure-service-account/) to use.
-
-`k8s.storageClaimName`
-: The name of the persistent volume claim where store workflow result data.
-
-`k8s.storageMountPath`
-: The path location used to mount the persistent volume claim (default: `/workspace`).
-
-`k8s.storageSubPath`
-: The path in the persistent volume to be mounted (default: `/`).
-
-`k8s.workDir`
-: Defines the path where the workflow temporary data is stored. This must be a path in a shared K8s persistent volume (default: `<user-dir>/work`).
-
-See the {ref}`k8s-page` page for more details.
-
-(config-mail)=
-
-### Scope `mail`
-
-The `mail` scope controls the mail server used to send email notifications.
-
-The following settings are available:
-
-`mail.debug`
-: When `true` enables Java Mail logging for debugging purpose.
-
-`mail.from`
-: Default email sender address.
-
-`mail.smtp.host`
-: Host name of the mail server.
-
-`mail.smtp.port`
-: Port number of the mail server.
-
-`mail.smtp.user`
-: User name to connect to the mail server.
-
-`mail.smtp.password`
-: User password to connect to the mail server.
-
-`mail.smtp.proxy.host`
-: Host name of an HTTP web proxy server that will be used for connections to the mail server.
-
-`mail.smtp.proxy.port`
-: Port number for the HTTP web proxy server.
-
-`mail.smtp.*`
-: Any SMTP configuration property supported by the [Java Mail API](https://javaee.github.io/javamail/), which Nextflow uses to send emails. See the table of available properties [here](https://javaee.github.io/javamail/docs/api/com/sun/mail/smtp/package-summary.html#properties).
-
-For example, the following snippet shows how to configure Nextflow to send emails through the [AWS Simple Email Service](https://aws.amazon.com/ses/):
+A configuration file can include any number of other configuration files using the `includeConfig` keyword:
 
 ```groovy
-mail {
-    smtp.host = 'email-smtp.us-east-1.amazonaws.com'
-    smtp.port = 587
-    smtp.user = '<Your AWS SES access key>'
-    smtp.password = '<Your AWS SES secret key>'
-    smtp.auth = true
-    smtp.starttls.enable = true
-    smtp.starttls.required = true
-}
-```
-
-:::{note}
-Some versions of Java (e.g. Java 11 Corretto) do not default to TLS v1.2, and as a result may have issues with 3rd party integrations that enforce TLS v1.2 (e.g. Azure Active Directory OIDC). This problem can be addressed by setting the following config option:
-
-```groovy
-mail {
-    smtp.ssl.protocols = 'TLSv1.2'
-}
-```
-:::
-
-(config-manifest)=
-
-### Scope `manifest`
-
-The `manifest` scope allows you to define some meta-data information needed when publishing or running your pipeline.
-
-The following settings are available:
-
-`manifest.author`
-: Project author name (use a comma to separate multiple names).
-
-`manifest.defaultBranch`
-: Git repository default branch (default: `master`).
-
-`manifest.description`
-: Free text describing the workflow project.
-
-`manifest.doi`
-: Project related publication DOI identifier.
-
-`manifest.homePage`
-: Project home page URL.
-
-`manifest.mainScript`
-: Project main script (default: `main.nf`).
-
-`manifest.name`
-: Project short name.
-
-`manifest.nextflowVersion`
-: Minimum required Nextflow version.
-
-  This setting may be useful to ensure that a specific version is used:
-
-  ```groovy
-  manifest.nextflowVersion = '1.2.3'        // exact match
-  manifest.nextflowVersion = '1.2+'         // 1.2 or later (excluding 2 and later)
-  manifest.nextflowVersion = '>=1.2'        // 1.2 or later
-  manifest.nextflowVersion = '>=1.2, <=1.5' // any version in the 1.2 .. 1.5 range
-  manifest.nextflowVersion = '!>=1.2'       // with ! prefix, stop execution if current version does not match required version.
-  ```
-
-`manifest.recurseSubmodules`
-: Pull submodules recursively from the Git repository.
-
-`manifest.version`
-: Project version number.
-
-The above options can also be specified in a `manifest` block, for example:
+process.executor = 'sge'
+process.queue = 'long'
+process.memory = '10G'
 
-```groovy
-manifest {
-    homePage = 'http://foo.com'
-    description = 'Pipeline does this and that'
-    mainScript = 'foo.nf'
-    version = '1.0.0'
-}
+includeConfig 'path/foo.config'
 ```
 
-Read the {ref}`sharing-page` page to learn how to publish your pipeline to GitHub, BitBucket or GitLab.
-
-(config-nextflow)=
-
-### Scope `nextflow`
+Relative paths are resolved against the location of the including file.
 
-The `nextflow` scope provides configuration options for the Nextflow runtime.
+:::{note}
+Config includes can also be specified within config blocks. However, config files should only be included at the top level or in a [profile](#config-profiles) so that the included config file is valid on its own and in the context in which it is included.
+:::
 
-`nextflow.publish.retryPolicy.delay`
-: :::{versionadded} 24.03.0-edge
-  :::
-: Delay when retrying a failed publish operation (default: `350ms`).
+## Constants
 
-`nextflow.publish.retryPolicy.jitter`
-: :::{versionadded} 24.03.0-edge
-  :::
-: Jitter value when retrying a failed publish operation (default: `0.25`).
+The following constants are globally available in a Nextflow configuration file:
 
-`nextflow.publish.retryPolicy.maxAttempt`
-: :::{versionadded} 24.03.0-edge
+`baseDir`
+: :::{deprecated} 20.04.0
   :::
-: Max attempts when retrying a failed publish operation (default: `5`).
-
-`nextflow.publish.retryPolicy.maxDelay`
-: :::{versionadded} 24.03.0-edge
-  :::
-: Max delay when retrying a failed publish operation (default: `90s`).
-
-(config-notification)=
-
-### Scope `notification`
-
-The `notification` scope allows you to define the automatic sending of a notification email message when the workflow execution terminates.
-
-`notification.attributes`
-: A map object modelling the variables that can be used in the template file.
-
-`notification.enabled`
-: Enables the sending of a notification message when the workflow execution completes.
+: Alias for `projectDir`.
 
-`notification.from`
-: Sender address for the notification email message.
+`launchDir`
+: The directory where the workflow was launched.
 
-`notification.template`
-: Path of a template file which provides the content of the notification message.
+`projectDir`
+: The directory where the main script is located.
 
-`notification.to`
-: Recipient address for the notification email. Multiple addresses can be specified separating them with a comma.
+## Functions
 
-The notification message is sent my using the STMP server defined in the configuration {ref}`mail scope<config-mail>`.
+The following functions are globally available in a Nextflow configuration file:
 
-If no mail configuration is provided, it tries to send the notification message by using the external mail command eventually provided by the underlying system (e.g. `sendmail` or `mail`).
+`env( name )`
+: :::{versionadded} 24.11.0-edge
+  :::
+: Get the value of the environment variable with the specified name in the Nextflow launch environment.
 
 (config-params)=
 
-### Scope `params`
+## Parameters
 
-The `params` scope allows you to define parameters that will be accessible in the pipeline script. Simply prefix the parameter names with the `params` scope or surround them by curly brackets, as shown below:
+Pipeline parameters can be defined in the config file using the `params` scope:
 
 ```groovy
 params.custom_param = 123
@@ -1338,48 +135,16 @@ params.another_param = 'string value .. '
 params {
     alpha_1 = true
     beta_2 = 'another string ..'
-}
-```
-
-(config-podman)=
-
-### Scope `podman`
-
-The `podman` scope controls how [Podman](https://podman.io/) containers are executed by Nextflow.
-
-The following settings are available:
-
-`podman.enabled`
-: Enable Podman execution (default: `false`).
-
-`podman.engineOptions`
-: This attribute can be used to provide any option supported by the Podman engine i.e. `podman [OPTIONS]`.
-
-`podman.envWhitelist`
-: Comma separated list of environment variable names to be included in the container environment.
-
-`podman.mountFlags`
-: Add the specified flags to the volume mounts e.g. `mountFlags = 'ro,Z'`.
-
-`podman.registry`
-: The registry from where container images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
-
-`podman.remove`
-: Clean-up the container after the execution (default: `true`).
-
-`podman.runOptions`
-: This attribute can be used to provide any extra command line options supported by the `podman run` command.
-
-`podman.temp`
-: Mounts a path of your choice as the `/tmp` directory in the container. Use the special value `auto` to create a temporary directory each time a container is created.
+}
+```
 
-Read the {ref}`container-podman` page to learn more about how to use Podman containers with Nextflow.
+See {ref}`cli-params` for information about how to modify these on the command line.
 
 (config-process)=
 
-### Scope `process`
+## Process configuration
 
-The `process` scope allows you to specify default {ref}`directives <process-directives>` for processes in your pipeline.
+The `process` scope allows you to specify {ref}`process directives <process-reference>` separately from the pipeline code.
 
 For example:
 
@@ -1395,7 +160,7 @@ By using this configuration, all processes in your pipeline will be executed thr
 
 (config-process-selectors)=
 
-#### Process selectors
+### Process selectors
 
 The `withLabel` selectors allow the configuration of all processes annotated with a {ref}`process-label` directive as shown below:
 
@@ -1433,7 +198,7 @@ Label and process names do not need to be enclosed with quotes, provided the nam
 
 (config-selector-expressions)=
 
-#### Selector expressions
+### Selector expressions
 
 Both label and process name selectors allow the use of a regular expression in order to apply the same configuration to all processes matching the specified pattern condition. For example:
 
@@ -1462,7 +227,7 @@ The above configuration snippet sets 2 cpus for the processes annotated with the
 
 (config-selector-priority)=
 
-#### Selector priority
+### Selector priority
 
 Process configuration settings are applied to a process in the following order (from lowest to highest priority):
 
@@ -1490,326 +255,6 @@ With the above configuration:
 - Any process named `bar` (or imported as `bar`) will use 16 cpus.
 - Any process named `bar` (or imported as `bar`) invoked by a workflow named `baz` with use 32 cpus.
 
-(config-report)=
-
-### Scope `report`
-
-The `report` scope allows you to configure the workflow {ref}`execution-report`.
-
-The following settings are available:
-
-`report.enabled`
-: If `true` it create the workflow execution report.
-
-`report.file`
-: The path of the created execution report file (default: `report-<timestamp>.html`).
-
-`report.overwrite`
-: When `true` overwrites any existing report file with the same name.
-
-(config-sarus)=
-
-### Scope `sarus`
-
-The ``sarus`` scope controls how [Sarus](https://sarus.readthedocs.io) containers are executed by Nextflow.
-
-The following settings are available:
-
-`sarus.enabled`
-: Enable Sarus execution (default: `false`).
-
-`sarus.envWhitelist`
-: Comma separated list of environment variable names to be included in the container environment.
-
-`sarus.runOptions`
-: This attribute can be used to provide any extra command line options supported by the `sarus run` command. For details see the [Sarus user guide](https://sarus.readthedocs.io/en/stable/user/user_guide.html).
-
-`sarus.tty`
-: Allocates a pseudo-tty (default: `false`).
-
-Read the {ref}`container-sarus` page to learn more about how to use Sarus containers with Nextflow.
-
-(config-shifter)=
-
-### Scope `shifter`
-
-The `shifter` scope controls how [Shifter](https://docs.nersc.gov/programming/shifter/overview/) containers are executed by Nextflow.
-
-The following settings are available:
-
-`shifter.enabled`
-: Enable Shifter execution (default: `false`).
-
-Read the {ref}`container-shifter` page to learn more about how to use Shifter containers with Nextflow.
-
-(config-singularity)=
-
-### Scope `singularity`
-
-The `singularity` scope controls how [Singularity](https://sylabs.io/singularity/) containers are executed by Nextflow.
-
-The following settings are available:
-
-`singularity.autoMounts`
-: When `true` Nextflow automatically mounts host paths in the executed container. It requires the `user bind control` feature to be enabled in your Singularity installation (default: `true`).
-: :::{versionchanged} 23.09.0-edge
-  Default value was changed from `false` to `true`.
-  :::
-
-`singularity.cacheDir`
-: The directory where remote Singularity images are stored. When using a computing cluster it must be a shared folder accessible to all compute nodes.
-
-`singularity.enabled`
-: Enable Singularity execution (default: `false`).
-
-`singularity.engineOptions`
-: This attribute can be used to provide any option supported by the Singularity engine i.e. `singularity [OPTIONS]`.
-
-`singularity.envWhitelist`
-: Comma separated list of environment variable names to be included in the container environment.
-
-`singularity.noHttps`
-: Pull the Singularity image with http protocol (default: `false`).
-
-`singularity.ociAutoPull`
-: :::{versionadded} 23.12.0-edge
-  :::
-: When enabled, OCI (and Docker) container images are pull and converted to a SIF image file format implicitly by the Singularity run command, instead of Nextflow. Requires Singularity 3.11 or later (default: `false`).
-
-  :::{note}
-  Leave `ociAutoPull` disabled if willing to build a Singularity native image with Wave (see the {ref}`wave-singularity` section).
-  :::
-
-`singularity.ociMode`
-: :::{versionadded} 23.12.0-edge
-  :::
-: Enable OCI-mode, that allows running native OCI compliant container image with Singularity using `crun` or `runc` as low-level runtime. Note: it requires Singularity 4 or later. See `--oci` flag in the [Singularity documentation](https://docs.sylabs.io/guides/4.0/user-guide/oci_runtime.html#oci-mode) for more details and requirements (default: `false`).
-
-  :::{note}
-  Leave `ociMode` disabled if you are willing to build a Singularity native image with Wave (see the {ref}`wave-singularity` section).
-  :::
-
-`singularity.pullTimeout`
-: The amount of time the Singularity pull can last, exceeding which the process is terminated (default: `20 min`).
-
-`singularity.registry`
-: :::{versionadded} 22.12.0-edge
-  :::
-: The registry from where Docker images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
-
-`singularity.runOptions`
-: This attribute can be used to provide any extra command line options supported by `singularity exec`.
-
-Read the {ref}`container-singularity` page to learn more about how to use Singularity containers with Nextflow.
-
-(config-spack)=
-
-### Scope `spack`
-
-The `spack` scope controls the creation of a Spack environment by the Spack package manager.
-
-The following settings are available:
-
-`spack.cacheDir`
-: Defines the path where Spack environments are stored. When using a compute cluster make sure to provide a shared file system path accessible from all compute nodes.
-
-`spack.checksum`
-: Enables checksum verification for source tarballs (default: `true`). Only disable when requesting a package version not yet encoded in the corresponding Spack recipe.
-
-`spack.createTimeout`
-: Defines the amount of time the Spack environment creation can last. The creation process is terminated when the timeout is exceeded (default: `60 min`).
-
-`spack.parallelBuilds`
-: Sets number of parallel package builds (Spack default: coincides with number of available CPU cores).
-
-Nextflow does not allow for fine-grained configuration of the Spack package manager. Instead, this has to be performed directly on the host Spack installation. For more information see the [Spack documentation](https://spack.readthedocs.io).
-
-(config-timeline)=
-
-### Scope `timeline`
-
-The `timeline` scope controls the execution timeline report generated by Nextflow.
-
-The following settings are available:
-
-`timeline.enabled`
-: When `true` enables the generation of the timeline report file (default: `false`).
-
-`timeline.file`
-: Timeline file name (default: `timeline-<timestamp>.html`).
-
-`timeline.overwrite`
-: When `true` overwrites any existing timeline file with the same name.
-
-(config-tower)=
-
-### Scope `tower`
-
-The `tower` scope controls the settings for the [Seqera Platform](https://seqera.io) (formerly Tower Cloud).
-
-The following settings are available:
-
-`tower.accessToken`
-: The unique access token specific to your account on an instance of Seqera Platform.
-
-  Your `accessToken` can be obtained from your Seqera Platform instance in the [Tokens page](https://cloud.seqera.io/tokens).
-
-`tower.enabled`
-: When `true` Nextflow sends the workflow tracing and execution metrics to Seqera Platform (default: `false`).
-
-`tower.endpoint`
-: The endpoint of your Seqera Platform instance (default: `https://api.cloud.seqera.io`).
-
-`tower.workspaceId`
-: The ID of the Seqera Platform workspace where the run should be added (default: the launching user personal workspace).
-
-  The workspace ID can also be specified using the environment variable `TOWER_WORKSPACE_ID` (config file has priority over the environment variable).
-
-(config-trace)=
-
-### Scope `trace`
-
-The `trace` scope controls the layout of the execution trace file generated by Nextflow.
-
-The following settings are available:
-
-`trace.enabled`
-: When `true` turns on the generation of the execution trace report file (default: `false`).
-
-`trace.fields`
-: Comma separated list of fields to be included in the report. The available fields are listed at {ref}`this page <trace-fields>`.
-
-`trace.file`
-: Trace file name (default: `trace-<timestamp>.txt`).
-
-`trace.overwrite`
-: When `true` overwrites any existing trace file with the same name.
-
-`trace.raw`
-: When `true` turns on raw number report generation i.e. date and time are reported as milliseconds and memory as number of bytes.
-
-`trace.sep`
-: Character used to separate values in each row (default: `\t`).
-
-The above options can also be specified in a `trace` block, for example:
-
-```groovy
-trace {
-    enabled = true
-    file = 'pipeline_trace.txt'
-    fields = 'task_id,name,status,exit,realtime,%cpu,rss'
-}
-```
-
-Read the {ref}`trace-report` page to learn more about the execution report that can be generated by Nextflow.
-
-(config-wave)=
-
-### Scope `wave`
-
-The `wave` scope provides advanced configuration for the use of {ref}`Wave containers <wave-page>`.
-
-The following settings are available:
-
-`wave.enabled`
-: Enable/disable the use of Wave containers.
-
-`wave.build.repository`
-: The container repository where images built by Wave are uploaded (note: the corresponding credentials must be provided in your Seqera Platform account).
-
-`wave.build.cacheRepository`
-: The container repository used to cache image layers built by the Wave service (note: the corresponding credentials must be provided in your Seqera Platform account).
-
-`wave.build.conda.basePackages`
-: One or more Conda packages to be always added in the resulting container (default: `conda-forge::procps-ng`).
-
-`wave.build.conda.commands`
-: One or more commands to be added to the Dockerfile used to build a Conda based image.
-
-`wave.build.conda.mambaImage`
-: The Mamba container image is used to build Conda based container. This is expected to be [micromamba-docker](https://github.com/mamba-org/micromamba-docker) image.
-
-`wave.build.spack.basePackages`
-: :::{versionadded} 22.06.0-edge
-  :::
-: One or more Spack packages to be always added in the resulting container.
-
-`wave.build.spack.commands`
-: :::{versionadded} 22.06.0-edge
-  :::
-: One or more commands to be added to the Dockerfile used to build a Spack based image.
-
-`wave.endpoint`
-: The Wave service endpoint (default: `https://wave.seqera.io`).
-
-`wave.freeze`
-: :::{versionadded} 23.07.0-edge
-  :::
-: Enables Wave container freezing. Wave will provision a non-ephemeral container image that will be pushed to a container repository of your choice. It requires the use of the `wave.build.repository` setting.
-: It is also recommended to specify a custom cache repository using `wave.build.cacheRepository`.
-: :::{note}
-  The container repository authentication must be managed by the underlying infrastructure.
-  :::
-
-`wave.httpClient.connectTime`
-: :::{versionadded} 22.06.0-edge
-  :::
-: Sets the connection timeout duration for the HTTP client connecting to the Wave service (default: `30s`).
-
-`wave.retryPolicy.delay`
-: :::{versionadded} 22.06.0-edge
-  :::
-: The initial delay when a failing HTTP request is retried (default: `150ms`).
-
-`wave.retryPolicy.jitter`
-: :::{versionadded} 22.06.0-edge
-  :::
-: The jitter factor used to randomly vary retry delays (default: `0.25`).
-
-`wave.retryPolicy.maxAttempts`
-: :::{versionadded} 22.06.0-edge
-  :::
-: The max number of attempts a failing HTTP request is retried (default: `5`).
-
-`wave.retryPolicy.maxDelay`
-: :::{versionadded} 22.06.0-edge
-  :::
-: The max delay when a failing HTTP request is retried (default: `90 seconds`).
-
-`wave.strategy`
-: The strategy to be used when resolving ambiguous Wave container requirements (default: `'container,dockerfile,conda,spack'`).
-
-### Scope `workflow`
-
-The `workflow` scope provides workflow execution options.
-
-`workflow.failOnIgnore`
-: :::{versionadded} 24.05.0-edge
-  :::
-: When `true`, the pipeline will exit with a non-zero exit code if any failed tasks are ignored using the `ignore` error strategy.
-
-(config-miscellaneous)=
-
-### Miscellaneous
-
-There are additional variables that can be defined within a configuration file that do not have a dedicated scope.
-
-`cleanup`
-: If `true`, on a successful completion of a run all files in *work* directory are automatically deleted.
-
-  :::{warning}
-  The use of the `cleanup` option will prevent the use of the *resume* feature on subsequent executions of that pipeline run. Also, be aware that deleting all scratch files can take a lot of time, especially when using a shared file system or remote cloud storage.
-  :::
-
-`dumpHashes`
-: If `true`, dump task hash keys in the log file, for debugging purposes. Equivalent to the `-dump-hashes` option of the `run` command.
-
-`resume`
-: If `true`, enable the use of previously cached task executions. Equivalent to the `-resume` option of the `run` command.
-
-`workDir`
-: Defines the pipeline work directory. Equivalent to the `-work-dir` option of the `run` command.
-
 (config-profiles)=
 
 ## Config profiles
@@ -1871,303 +316,20 @@ profiles {
 In the above example, the `process.cpus` attribute is not correctly applied because the `process` scope is also used in the `foo` and `bar` profiles.
 :::
 
-(config-env-vars)=
-
-## Environment variables
-
-The following environment variables control the configuration of the Nextflow runtime and the underlying Java virtual machine.
-
-`NXF_ANSI_LOG`
-: Enables/disables ANSI console output (default `true` when ANSI terminal is detected).
-
-`NXF_ANSI_SUMMARY`
-: Enables/disables ANSI completion summary: `true\|false` (default: print summary if execution last more than 1 minute).
-
-`NXF_ASSETS`
-: Defines the directory where downloaded pipeline repositories are stored (default: `$NXF_HOME/assets`)
-
-`NXF_CACHE_DIR`
-: :::{versionadded} 24.02.0-edge
-  :::
-: Defines the base cache directory when using the default cache store (default: `"$launchDir/.nextflow"`).
-
-`NXF_CHARLIECLOUD_CACHEDIR`
-: Directory where remote Charliecloud images are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
-
-`NXF_CLOUDCACHE_PATH`
-: :::{versionadded} 23.07.0-edge
-  :::
-: Defines the base cache path when using the cloud cache store.
-
-`NXF_CLOUD_DRIVER`
-: Defines the default cloud driver to be used if not specified in the config file or as command line option, either `aws` or `google`.
-
-`NXF_CONDA_CACHEDIR`
-: Directory where Conda environments are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
-
-`NXF_CONDA_ENABLED`
-: :::{versionadded} 22.08.0-edge
-  :::
-: Enable the use of Conda recipes defined by using the {ref}`process-conda` directive. (default: `false`).
-
-`NXF_DEFAULT_DSL`
-: :::{versionadded} 22.03.0-edge
-  :::
-: Defines the DSL version that should be used in not specified otherwise in the script of config file (default: `2`)
-
-`NXF_DISABLE_CHECK_LATEST`
-: :::{versionadded} 23.09.0-edge
-  :::
-: Nextflow automatically checks for a newer version of itself unless this option is enabled (default: `false`).
-
-`NXF_DISABLE_JOBS_CANCELLATION`
-: :::{versionadded} 21.12.0-edge
-  :::
-: Disables the cancellation of child jobs on workflow execution termination.
-
-`NXF_DISABLE_PARAMS_TYPE_DETECTION`
-: :::{versionadded} 23.07.0-edge
-  :::
-: Disables the automatic type detection of command line parameters.
-
-`NXF_DISABLE_WAVE_SERVICE`
-: :::{versionadded} 23.08.0-edge
-  :::
-: Disables the requirement for Wave service when enabling the Fusion file system.
-
-`NXF_ENABLE_AWS_SES`
-: :::{versionadded} 23.06.0-edge
-  :::
-: Enable to use of AWS SES native API for sending emails in place of legacy SMTP settings (default: `false`)
-
-`NXF_ENABLE_FS_SYNC`
-: :::{versionadded} 23.10.0
-  :::
-: When enabled the job script will execute Linux `sync` command on job completion. This may be useful to synchronize the job state over shared file systems (default: `false`)
-
-`NXF_ENABLE_SECRETS`
-: :::{versionadded} 21.09.0-edge
-  :::
-: Enable Nextflow secrets features (default: `true`)
-
-`NXF_ENABLE_STRICT`
-: :::{versionadded} 22.05.0-edge
-  :::
-: Enable Nextflow *strict* execution mode (default: `false`)
-
-`NXF_ENABLE_VIRTUAL_THREADS`
-: :::{versionadded} 23.05.0-edge
-  :::
-: :::{versionchanged} 23.10.0
-  Enabled by default when using Java 21 or later.
-  :::
-: Enable the use of virtual threads in the Nextflow runtime (default: `false`)
-
-`NXF_EXECUTOR`
-: Defines the default process executor, e.g. `sge`
-
-`NXF_FILE_ROOT`
-: :::{versionadded} 23.05.0-edge
-  :::
-: The file storage path against which relative file paths are resolved.
-: For example, with `NXF_FILE_ROOT=/some/root/path`, the use of `file('foo')` will be resolved to the absolute path `/some/root/path/foo`. A remote root path can be specified using the usual protocol prefix, e.g. `NXF_FILE_ROOT=s3://my-bucket/data`. Files defined using an absolute path are not affected by this setting.
-
-`NXF_HOME`
-: Nextflow home directory (default: `$HOME/.nextflow`).
-
-`NXF_JAVA_HOME`
-: Defines the path location of the Java VM installation used to run Nextflow. This variable overrides the `JAVA_HOME` variable if defined.
-
-`NXF_JVM_ARGS`
-: :::{versionadded} 21.12.1-edge
-  :::
-: Allows the setting Java VM options. This is similar to `NXF_OPTS` however it's only applied the JVM running Nextflow and not to any java pre-launching commands.
-
-`NXF_LOG_FILE`
-: The filename of the Nextflow log (default: `.nextflow.log`)
-
-`NXF_OFFLINE`
-: When `true` prevents Nextflow from automatically downloading and updating remote project repositories (default: `false`).
-: :::{versionchanged} 23.09.0-edge
-  This option also disables the automatic version check (see `NXF_DISABLE_CHECK_LATEST`).
-  :::
-: :::{versionchanged} 23.11.0-edge
-  This option also prevents plugins from being downloaded. Plugin versions must be specified in offline mode, or else Nextflow will fail.
-  :::
-
-`NXF_OPTS`
-: Provides extra options for the Java and Nextflow runtime. It must be a blank separated list of `-Dkey[=value]` properties.
-
-`NXF_ORG`
-: Default `organization` prefix when looking for a hosted repository (default: `nextflow-io`).
-
-`NXF_PARAMS_FILE`
-: :::{versionadded} 20.10.0
-  :::
-: Defines the path location of the pipeline parameters file .
-
-`NXF_PID_FILE`
-: Name of the file where the process PID is saved when Nextflow is launched in background.
-
-`NXF_PLUGINS_DEFAULT`
-: Whether to use the default plugins when no plugins are specified in the Nextflow configuration (default: `true`).
-
-`NXF_PLUGINS_DIR`
-: The path where the plugin archives are loaded and stored (default: `$NXF_HOME/plugins`).
-
-`NXF_PLUGINS_TEST_REPOSITORY`
-: :::{versionadded} 23.04.0
-  :::
-: Defines a custom plugin registry or plugin release URL for testing plugins outside of the main registry. See {ref}`testing-plugins` for more information.
-
-`NXF_PUBLISH_FAIL_ON_ERROR`
-: :::{versionadded} 24.04.3
-  :::
-: Defines the default behavior of `publishDir.failOnError` setting. See {ref}`publishDir<process-publishdir>` directive for more information.
-
-`NXF_SCM_FILE`
-: :::{versionadded} 20.10.0
-  :::
-: Defines the path location of the SCM config file .
-
-`NXF_SINGULARITY_CACHEDIR`
-: Directory where remote Singularity images are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
-
-`NXF_SINGULARITY_LIBRARYDIR`
-: :::{versionadded} 21.09.0-edge
-  :::
-: Directory where remote Singularity images are retrieved. It should be a directory accessible to all compute nodes.
-
-`NXF_SPACK_CACHEDIR`
-: Directory where Spack environments are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
-
-`NXF_SPACK_ENABLED`
-: :::{versionadded} 23.02.0-edge
-  :::
-: Enable the use of Spack recipes defined by using the {ref}`process-spack` directive. (default: `false`).
-
-`NXF_TEMP`
-: Directory where temporary files are stored
-
-`NXF_TRACE`
-: Enable trace level logging for the specified packages. Equivalent to the `-trace` command-line option.
-
-`NXF_VER`
-: Defines which version of Nextflow to use.
-
-`NXF_WORK`
-: Directory where working files are stored (usually your *scratch* directory)
-
-`NXF_WRAPPER_STAGE_FILE_THRESHOLD`
-: :::{versionadded} 23.05.0-edge
-  :::
-: Defines the minimum size of the `.command.run` staging script for it to be written to a separate `.command.stage` file (default: `'1 MB'`).
-: This setting is useful for executors that impose a size limit on job scripts.
-
-`JAVA_HOME`
-: Defines the path location of the Java VM installation used to run Nextflow.
-
-`JAVA_CMD`
-: Defines the path location of the Java binary command used to launch Nextflow.
-
-`HTTP_PROXY`
-: Defines the HTTP proxy server.
-: :::{versionadded} 21.06.0-edge
-  Proxy authentication is supported by providing the credentials in the proxy URL, e.g. `http://user:password@proxy-host.com:port`.
-  :::
-
-`HTTPS_PROXY`
-: Defines the HTTPS proxy server.
-: :::{versionadded} 21.06.0-edge
-  Proxy authentication is supported by providing the credentials in the proxy URL, e.g. `https://user:password@proxy-host.com:port`.
-  :::
-
-`FTP_PROXY`
-: :::{versionadded} 21.06.0-edge
-  :::
-: Defines the FTP proxy server. Proxy authentication is supported by providing the credentials in the proxy URL, e.g. `ftp://user:password@proxy-host.com:port`.
-
-`NO_PROXY`
-: Defines one or more host names that should not use the proxy server. Separate multiple names using a comma character.
-
-(config-feature-flags)=
-
-## Feature flags
-
-Some features can be enabled using the `nextflow.enable` and `nextflow.preview` flags. These flags can be specified in the pipeline script or the configuration file, and they are generally used to introduce experimental or other opt-in features.
-
-`nextflow.enable.configProcessNamesValidation`
-
-: When `true`, prints a warning for every `withName:` process selector that doesn't match a process in the pipeline (default: `true`).
-
-`nextflow.enable.dsl`
-
-: Defines the DSL version to use (`1` or `2`).
-
-: :::{versionadded} 22.03.0-edge
-  DSL2 is the default DSL version.
-  :::
-
-: :::{versionadded} 22.12.0-edge
-  DSL1 is no longer supported.
-  :::
-
-`nextflow.enable.moduleBinaries`
-
-: When `true`, enables the use of modules with binary scripts. See {ref}`module-binaries` for more information.
-
-`nextflow.enable.strict`
-
-: :::{versionadded} 22.05.0-edge
-  :::
-
-: When `true`, the pipeline is executed in "strict" mode, which introduces the following rules:
-
-  - When reading a params file, Nextflow will fail if a dynamic param value references an undefined variable
-
-  - When merging params from a config file with params from the command line, Nextflow will fail if a param is specified from both sources but with different types
-
-  - When using the `join` operator, the `failOnDuplicate` option is `true` regardless of any user setting
-
-  - When using the `join` operator, the `failOnMismatch` option is `true` (unless `remainder` is also `true`) regardless of any user setting
-
-  - When using the `publishDir` process directive, the `failOnError` option is `true` regardless of any user setting
-
-  - In a process definition, Nextflow will fail if an input or output tuple has only one element
-
-  - In a process definition, Nextflow will fail if an output emit name is not a valid identifier (i.e. it should match the pattern `/[A-Za-z_][A-Za-z0-9_]*/`)
-
-  - During a process execution, Nextflow will fail if a received input tuple does not have the same number of elements as was declared
-
-  - During a process execution, Nextflow will fail if the `storeDir` directive is used with non-file outputs
-
-  - Nextflow will fail if a pipeline param is referenced before it is defined
+## Workflow handlers
 
-  - Nextflow will fail if multiple functions and/or processes with the same name are defined in a module script
+Workflow event handlers can be defined in the config file, which is useful for handling pipeline events without having to modify the pipeline code:
 
-`nextflow.preview.output`
-
-: :::{versionadded} 24.04.0
-  :::
-
-: *Experimental: may change in a future release.*
-
-: When `true`, enables the use of the {ref}`workflow output definition <workflow-output-def>`.
-
-`nextflow.preview.recursion`
-
-: :::{versionadded} 21.11.0-edge
-  :::
-
-: *Experimental: may change in a future release.*
-
-: When `true`, enables process and workflow recursion. See [this GitHub discussion](https://github.com/nextflow-io/nextflow/discussions/2521) for more information.
-
-`nextflow.preview.topic`
-
-: :::{versionadded} 23.11.0-edge
-  :::
+```groovy
+workflow.onComplete = {
+    // any workflow property can be used here
+    println "Pipeline complete"
+    println "Command line: $workflow.commandLine"
+}
 
-: *Experimental: may change in a future release.*
+workflow.onError = {
+    println "Error: something when wrong"
+}
+```
 
-: When `true`, enables {ref}`topic channels <channel-topic>` feature.
+See {ref}`workflow-handlers` for more information.
diff --git a/docs/container.md b/docs/container.md
index 1d0ad99e51..ba8a563828 100644
--- a/docs/container.md
+++ b/docs/container.md
@@ -94,7 +94,7 @@ Read the {ref}`Process scope <config-process>` section to learn more about proce
 
 Nextflow is able to transparently pull remote container images stored in any Docker compatible registry.
 
-By default when a container name is specified, Nextflow checks if an image file with that name exists in the local file system. If that image file exists, it's used to execute the container. If a matching file does not exist, Nextflow automatically tries to pull an image with the specified name from the container registry.
+By default, when a container name is specified, Nextflow checks if an image file with that name exists in the local file system. If that image file exists, it's used to execute the container. If a matching file does not exist, Nextflow automatically tries to pull an image with the specified name from the container registry.
 
 If you want Nextflow to check only for local file images, prefix the container name with the `file://` pseudo-protocol. For example:
 
@@ -107,7 +107,7 @@ apptainer.enabled = true
 Use three `/` slashes to specify an **absolute** file path, otherwise the path will be interpreted as relative to the workflow launch directory.
 :::
 
-To pull images from Apptainer Hub or a third party Docker registry, simply prefix the image name with the `shub://`, `docker://` or `docker-daemon://` pseudo-protocol as required by Apptainer. For example:
+To pull images from Apptainer Hub or a third party Docker registry, prefix the image name with the `shub://`, `docker://` or `docker-daemon://` pseudo-protocol as required by Apptainer. For example:
 
 ```groovy
 process.container = 'docker://quay.io/biocontainers/multiqc:1.3--py35_2'
@@ -120,11 +120,11 @@ You do not need to specify `docker://` to pull from a Docker repository. Nextflo
 This feature requires the `apptainer` tool to be installed where the workflow execution is launched (as opposed to the compute nodes).
 :::
 
-Nextflow caches those images in the `apptainer` directory in the pipeline work directory by default. However it is suggested to provide a centralised cache directory by using either the `NXF_APPTAINER_CACHEDIR` environment variable or the `apptainer.cacheDir` setting in the Nextflow config file.
+Nextflow caches Apptainer images in the `apptainer` directory, in the pipeline work directory, by default. However, it is recommended to provide a centralized cache directory using the `NXF_APPTAINER_CACHEDIR` environment variable or the `apptainer.cacheDir` setting in the Nextflow config file.
 
-:::{versionadded} 21.09.0-edge
-When looking for a Apptainer image file, Nextflow first checks the *library* directory, and if the image file is not found, the *cache* directory is used s usual. The library directory can be defined either using the `NXF_APPTAINER_LIBRARYDIR` environment variable or the `apptainer.libraryDir` configuration setting (the latter overrides the former).
-:::
+Nextflow uses the library directory to determine the location of Apptainer containers. The library directory can be defined using the `apptainer.libraryDir` configuration setting or the `NXF_APPTAINER_LIBRARYDIR` environment variable. The configuration file option overrides the environment variable if both are set.
+
+Nextflow first checks the library directory when searching for the image. If the image is not found it then checks the cache directory. The main difference between the library directory and the cache directory is that the first is assumed to be a read-only container repository, while the latter is expected to be writable path where container images can added for caching purposes.
 
 :::{warning}
 When using a compute cluster, the Apptainer cache directory must reside in a shared filesystem accessible to all compute nodes.
@@ -293,17 +293,19 @@ It is possible to specify a different Docker image for each process definition i
 process foo {
   container 'image_name_1'
 
-  '''
+  script:
+  """
   do this
-  '''
+  """
 }
 
 process bar {
   container 'image_name_2'
 
-  '''
+  script:
+  """
   do that
-  '''
+  """
 }
 ```
 
@@ -380,17 +382,19 @@ It is possible to specify a different container image for each process definitio
 process foo {
   container 'image_name_1'
 
-  '''
+  script:
+  """
   do this
-  '''
+  """
 }
 
 process bar {
   container 'image_name_2'
 
-  '''
+  script:
+  """
   do that
-  '''
+  """
 }
 ```
 
@@ -649,11 +653,11 @@ process.container = 'library://library/default/alpine:3.8'
 
 The `library://` pseudo-protocol allows you to import Singularity images from a local Docker installation instead of downloading them from a Docker registry. This feature requires the `singularity` tool to be installed where the workflow execution is launched (as opposed to the compute nodes).
 
-Nextflow caches the images in `${NXF_WORK}/singularity` by default. However, it is recommended to define a centralised cache directory using either the `NXF_SINGULARITY_CACHEDIR` environment variable or the `singularity.cacheDir` setting in the Nextflow config file.
+Nextflow caches Singularity images in the `singularity` directory, in the pipeline work directory, by default. However, it is recommended to provide a centralized cache directory using the `NXF_SINGULARITY_CACHEDIR` environment variable or the `singularity.cacheDir` setting in the Nextflow config file.
 
-:::{versionadded} 21.09.0-edge
-When looking for a Singularity image file, Nextflow first checks the *library* directory, and if the image file is not found, the *cache* directory is used as usual. The library directory can be defined either using the `NXF_SINGULARITY_LIBRARYDIR` environment variable or the `singularity.libraryDir` configuration setting (the latter overrides the former).
-:::
+Nextflow uses the library directory to determine the location of Singularity images. The library directory can be defined using the `singularity.libraryDir` configuration setting or the `NXF_SINGULARITY_LIBRARYDIR` environment variable. The configuration file option overrides the environment variable if both are set.
+
+Nextflow first checks the library directory when searching for the image. If the image is not found it then checks the cache directory. The main difference between the library directory and the cache directory is that the first is assumed to be a read-only container repository, while the latter is expected to be writable path where container images can added for caching purposes.
 
 :::{warning}
 When using a compute cluster, the Singularity cache directory must reside in a shared filesystem accessible to all compute nodes.
diff --git a/docs/developer/diagram.md b/docs/developer/diagram.md
index 9b895d0f7b..90300113c2 100644
--- a/docs/developer/diagram.md
+++ b/docs/developer/diagram.md
@@ -2,7 +2,7 @@
 
 # Workflow Diagram
 
-The following diagram is a high-level overview of the Nextflow source code in a similar style as the {ref}`workflow diagram <dag-visualisation>` visualization for Nextflow pipelines. Each node and subgraph is a class. Arrows depict the flow of data and/or communication between classes.
+The following diagram is a high-level overview of the Nextflow source code in a similar style as the {ref}`workflow diagram <workflow-diagram>` visualization for Nextflow pipelines. Each node and subgraph is a class. Arrows depict the flow of data and/or communication between classes.
 
 In general, nodes with sharp corners are "record" classes that simply hold information, while nodes with rounded edges are "function" classes that transform some input into an output. Subgraphs are either long-running classes, i.e. "places where things happen", or one of the other two types for which it was useful to expand and show internal details.
 
diff --git a/docs/developer/index.md b/docs/developer/index.md
index 48d22817ae..2f5a93f8b2 100644
--- a/docs/developer/index.md
+++ b/docs/developer/index.md
@@ -144,7 +144,7 @@ If you need to test changes to the `nextflow` launcher script, you can run it di
 
 ### Groovy REPL
 
-The `groovysh` command provides a command-line REPL that you can use to play around with Groovy code independently of Nextflow. The `groovyConsole` command provides a graphical REPL similar to `nextflow console`. These commands require a standalone Groovy distribution, which can be installed as described for Java in {ref}`Getting started <install-requirements>`.
+The `groovysh` command provides a command-line REPL that you can use to play around with Groovy code independently of Nextflow. The `groovyConsole` command provides a graphical REPL similar to `nextflow console`. These commands require a standalone Groovy distribution, which can be installed as described for Java on the {ref}`Installation <install-requirements>` page.
 
 :::{note}
 If you are using WSL, you must also install an X server for Windows, such as [VcXsrv](https://sourceforge.net/projects/vcxsrv/) or [Xming](http://www.straightrunning.com/XmingNotes/), in order to use these commands.
diff --git a/docs/developer/nextflow.ast.md b/docs/developer/nextflow.ast.md
index 5048ca6a8d..2b3bad9150 100644
--- a/docs/developer/nextflow.ast.md
+++ b/docs/developer/nextflow.ast.md
@@ -25,13 +25,14 @@ You can see the effect of Nextflow's AST transforms by using the Nextflow consol
 
 Here is the example from {ref}`your-first-script`:
 
-```groovy
+```nextflow
 params.str = 'Hello world!'
 
 process splitLetters {
   output:
     path 'chunk_*'
 
+  script:
   """
   printf '${params.str}' | split -b 6 - chunk_
   """
@@ -43,6 +44,7 @@ process convertToUpper {
   output:
     stdout
 
+  script:
   """
   cat $x | tr '[a-z]' '[A-Z]'
   """
@@ -62,6 +64,7 @@ process( splitLetters( {
   output:
     path('chunk_*')
 
+  script:
   """
   printf '${params.str}' | split -b 6 - chunk_
   """
@@ -73,6 +76,7 @@ process( convertToUpper( {
   output:
     stdout
 
+  script:
   """
   cat $x | tr '[a-z]' '[A-Z]'
   """
diff --git a/docs/developer/nextflow.dag.md b/docs/developer/nextflow.dag.md
index 2a79127f08..b08328c32a 100644
--- a/docs/developer/nextflow.dag.md
+++ b/docs/developer/nextflow.dag.md
@@ -16,4 +16,4 @@ Some classes may be excluded from the above diagram for brevity.
 
 The workflow DAG defines the network of processes, channels, and operators that comprise a workflow. It is produced by the execution of the Nextflow script. See [nextflow.script](nextflow.script.md) for more details.
 
-Implementations of the `DagRenderer` interface define how to render the workflow DAG to a particular diagram format. See {ref}`dag-visualisation` for more details.
+Implementations of the `DagRenderer` interface define how to render the workflow DAG to a particular diagram format. See {ref}`workflow-diagram` for more details.
diff --git a/docs/developer/nextflow.md b/docs/developer/nextflow.md
index 457df76a8c..6e973764b4 100644
--- a/docs/developer/nextflow.md
+++ b/docs/developer/nextflow.md
@@ -14,7 +14,7 @@ Some classes may be excluded from the above diagram for brevity.
 
 ## Notes
 
-The `Nextflow` class implements several methods that are exposed to Nextflow scripts. See {ref}`implicit-functions` for details.
+The `Nextflow` class implements several methods that are exposed to Nextflow scripts. See {ref}`stdlib-functions` for details.
 
 The `Channel` class implements the channel factory methods, and it is exposed directly to Nextflow scripts. See {ref}`channel-page` for details.
 
diff --git a/docs/developer/plugins.md b/docs/developer/plugins.md
index 99b0c2ee2b..5a95ec8f0f 100644
--- a/docs/developer/plugins.md
+++ b/docs/developer/plugins.md
@@ -1,11 +1,13 @@
 
-# Core plugins
+# Plugins
 
-This page describes the build process for Nextflow core plugins. See the {ref}`plugins-page` page to learn how to create your own plugins outside of Nextflow.
+This page describes how to create, test, and publish third-party plugins.
 
-## Plugin subprojects
+## Plugin structure
 
-Each plugin subproject has its own `build.gradle` which defines the main build actions and the required dependencies.
+The best way to get started with your own plugin is to refer to the [nf-hello](https://github.com/nextflow-io/nf-hello) repository. This repository provides a minimal plugin implementation with several examples of different extension points and instructions for building, testing, and publishing.
+
+Plugins can be written in Java or Groovy.
 
 The minimal dependencies are as follows:
 
@@ -16,8 +18,8 @@ dependencies {
     compileOnly 'org.pf4j:pf4j:3.4.1'
 
     testImplementation project(':nextflow')
-    testImplementation "org.codehaus.groovy:groovy:3.0.5"
-    testImplementation "org.codehaus.groovy:groovy-nio:3.0.5"
+    testImplementation "org.codehaus.groovy:groovy:4.0.24"
+    testImplementation "org.codehaus.groovy:groovy-nio:4.0.23"
 }
 ```
 
@@ -31,54 +33,332 @@ Plugin-Provider: Your Name or Organization
 Plugin-Version: 0.0.0
 ```
 
-## Environment variables
+## Extension points
 
-`NXF_PLUGINS_MODE`
-: The plugin execution mode, either `prod` for production or `dev` for development (see below for details).
+Nextflow's plugin system exposes a variety of extension points for plugins. This section describes how to use these extension points when writing a plugin, as well as how they are used in a pipeline.
 
-`NXF_PLUGINS_DIR`
-: The path where the plugin archives are loaded and stored (default: `$NXF_HOME/plugins` in production, `./plugins` in development).
+:::{note}
+If you would like to implement something in a plugin that isn't covered by any of the following sections, feel free to create an issue on GitHub and describe your use case. In general, any class in the Nextflow codebase that implements `ExtensionPoint` can be extended by a plugin, and existing plugins are a great source of examples when writing new plugins.
+:::
 
-`NXF_PLUGINS_DEFAULT`
-: Whether to use the default plugins when no plugins are specified in the Nextflow configuration (default: `true`).
+:::{note}
+Plugin extension points must be added to `extensions.idx` in the plugin repository to make them discoverable. See the [`nf-hello`](https://github.com/nextflow-io/nf-hello) plugin for an example.
+:::
 
-`NXF_PLUGINS_DEV`
-: Comma-separated list of development plugin root directories.
+### Commands
 
-## Development environment
+Plugins can define custom CLI commands that can be executed with the `nextflow plugin` command.
 
-When running in development mode, the plugin system uses the `DevPluginClasspath` to load plugin classes from each plugin project build path, e.g. `plugins/nf-amazon/build/classes` and `plugins/nf-amazon/build/target/libs` (for deps libraries).
+To implement a plugin-specific command, implement the `PluginExecAware` interface in your plugin entrypoint (the class that extends `BasePlugin`). Alternatively, you can implement the `PluginAbstractExec` trait, which provides an abstract implementation with some boilerplate code. This trait requires you to implement two methods, `getCommands()` and `exec()`:
 
-## Plugin registry
+```groovy
+import nextflow.cli.PluginAbstractExec
+import nextflow.plugin.BasePlugin
+
+class MyPlugin extends BasePlugin implements PluginAbstractExec {
+    @Override
+    List<String> getCommands() {
+        [ 'hello' ]
+    }
+
+    @Override
+    int exec(String cmd, List<String> args) {
+        if( cmd == 'hello' ) {
+            println "Hello! You gave me these arguments: ${args.join(' ')}"
+            return 0
+        }
+        else {
+            System.err.println "Invalid command: ${cmd}"
+            return 1
+        }
+    }
+}
+```
 
-The metadata for each plugin is published to the [nextflow-io/plugins](https://github.com/nextflow-io/plugins) GitHub repository, specifically [this file](https://raw.githubusercontent.com/nextflow-io/plugins/main/plugins.json).
+You can then execute this command using the `nextflow plugin` command:
 
-The repository index has the following structure:
+```bash
+nextflow plugin my-plugin:hello --foo --bar
+```
 
-```json
-[
-  {
-    "id": "nf-amazon",
-    "releases": [
-      {
-        "version": "0.2.0",
-        "url": "https://github.com/nextflow-io/nf-amazon/releases/download/0.2.0/nf-amazon-0.2.0.zip",
-        "date": "2020-10-12T10:05:44.28+02:00",
-        "sha512sum": "9e9e33695c1a7c051271..."
-      }
-    ]
-  },
-  /* ... */
-]
+See the {ref}`cli-plugin` CLI command for usage information.
+
+### Configuration
+
+Plugins can access the resolved Nextflow configuration through the session object using `session.config.navigate()`. Several extension points provide the session object for this reason. This method allows you to query any configuration option in a safe manner -- if the option isn't defined, it will return `null`. A common practice is to define any configuration for your plugin in a custom config scope.
+
+For example, you can query a config option in a trace observer hook:
+
+```groovy
+import nextflow.Session
+import nextflow.trace.TraceObserver
+
+class MyObserver implements TraceObserver {
+
+    @Override
+    void onFlowCreate(Session session) {
+        final message = session.config.navigate('myplugin.create.message')
+        println message
+    }
+}
+```
+
+You can then set this option in your config file:
+
+```groovy
+// dot syntax
+myplugin.create.message = "I'm alive!"
+
+// closure syntax
+myplugin {
+    create {
+        message = "I'm alive!"
+    }
+}
+```
+
+### Executors
+
+Plugins can define custom executors that can then be used with the `executor` process directive.
+
+To implement an executor, create a class in your plugin that extends the [`Executor`](https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/executor/Executor.groovy) class and implements the `ExtensionPoint` interface. Add the `@ServiceName` annotation to your class with the name of your executor:
+
+```groovy
+import nextflow.executor.Executor
+import nextflow.util.ServiceName
+import org.pf4j.ExtensionPoint
+
+@ServiceName('my-executor')
+class MyExecutor extends Executor implements ExtensionPoint {
+
+    // ...
+
+}
+```
+
+You can then use this executor in your pipeline:
+
+```nextflow
+process foo {
+    executor 'my-executor'
+
+    // ...
+}
+```
+
+:::{tip}
+Refer to the source code of Nextflow's built-in executors to see how to implement the various components of an executor. You might be able to implement most of your executor by simply reusing existing code.
+:::
+
+### Functions
+
+:::{versionadded} 22.09.0-edge
+:::
+
+Plugins can define custom functions, which can then be included in Nextflow pipelines.
+
+To implement a custom function, create a class in your plugin that extends the `PluginExtensionPoint` class, and implement your function with the `Function` annotation:
+
+```groovy
+import nextflow.Session
+import nextflow.plugin.extension.Function
+import nextflow.plugin.extension.PluginExtensionPoint
+
+class MyExtension extends PluginExtensionPoint {
+
+    @Override
+    void init(Session session) {}
+
+    @Function
+    String reverseString(String origin) {
+        origin.reverse()
+    }
+
+}
+```
+
+You can then use this function in your pipeline:
+
+```nextflow
+include { reverseString } from 'plugin/my-plugin'
+
+channel.of( reverseString('hi') )
+```
+
+You can also use an alias:
+
+```nextflow
+include { reverseString as anotherReverseMethod } from 'plugin/my-plugin'
+```
+
+### Operators
+
+:::{versionadded} 22.04.0
+:::
+
+Plugins can define custom channel factories and operators, which can then be included into Nextflow pipelines.
+
+To implement a custom factory or operator, create a class in your plugin that extends the `PluginExtensionPoint` class, and implement your function with the `Factory` or `Operator` annotation:
+
+```groovy
+import groovyx.gpars.dataflow.DataflowReadChannel
+import groovyx.gpars.dataflow.DataflowWriteChannel
+import nextflow.Session
+import nextflow.plugin.extension.Factory
+import nextflow.plugin.extension.Operator
+import nextflow.plugin.extension.PluginExtensionPoint
+
+class MyExtension extends PluginExtensionPoint {
+
+    @Override
+    void init(Session session) {}
+
+    @Factory
+    DataflowWriteChannel fromQuery(Map opts, String query) {
+        // ...
+    }
+
+    @Operator
+    DataflowWriteChannel sqlInsert(DataflowReadChannel source, Map opts) {
+        // ...
+    }
+
+}
+```
+
+You can then use them in your pipeline:
+
+```nextflow
+include { sqlInsert; fromQuery as fromTable } from 'plugin/nf-sqldb'
+
+def sql = 'select * from FOO'
+channel
+    .fromTable(sql, db: 'test', emitColumns: true)
+    .sqlInsert(into: 'BAR', columns: 'id', db: 'test')
+```
+
+The above snippet is based on the [nf-sqldb](https://github.com/nextflow-io/nf-sqldb) plugin. The `fromQuery` factory 
+is included under the alias `fromTable`.
+
+### Process directives
+
+Plugins that implement a [custom executor](#executors) will likely need to access {ref}`process directives <process-directives>` that affect the task execution. When an executor receives a task, the process directives can be accessed through that task's configuration. As a best practice, custom executors should try to support all process directives that have executor-specific behavior and are relevant to your executor.
+
+Nextflow does not provide the ability to define custom process directives in a plugin. Instead, you can use the {ref}`process-ext` directive to provide custom process settings to your executor. Try to use specific names that are not likely to conflict with other plugins or existing pipelines.
+
+For example, a custom executor can use existing process directives as well as a custom setting through the `ext` directive:
+
+```groovy
+class MyExecutor extends Executor {
+
+    @Override
+    TaskHandler createTaskHandler(TaskRun task) {
+        final cpus = task.config.cpus
+        final memory = task.config.memory
+        final myOption = task.config.ext.myOption
+
+        println "This task is configured with cpus=${cpus}, memory=${memory}, myOption=${myOption}"
+
+        // ...
+    }
+
+    // ...
+
+}
+```
+
+### Trace observers
+
+A *trace observer* in Nextflow is an entity that can listen and react to workflow events, such as when a workflow starts, a task completes, a file is published, etc. Several components in Nextflow, such as the execution report and DAG visualization, are implemented as trace observers.
+
+Plugins can define custom trace observers that react to workflow events with custom behavior. To implement a trace observer, create a class that implements the `TraceObserver` trait and another class that implements the `TraceObserverFactory` interface. Implement any of the hooks defined in `TraceObserver`, and implement the `create()` method in your observer factory:
+
+```groovy
+// MyObserverFactory.groovy
+import nextflow.Session
+import nextflow.trace.TraceObserver
+import nextflow.trace.TraceObserverFactory
+
+class MyObserverFactory implements TraceObserverFactory {
+
+    @Override
+    Collection<TraceObserver> create(Session session) {
+        final enabled = session.config.navigate('myplugin.enabled')
+        return enabled ? [ new MyObserver() ] : []
+    }
+}
+
+// MyObserver.groovy
+import java.nio.file.Path
+
+import nextflow.processor.TaskHandler
+import nextflow.trace.TraceObserver
+import nextflow.trace.TraceRecord
+
+class MyObserver implements TraceObserver {
+    
+    @Override
+    void onFlowBegin() {
+        println "Okay, let's begin!"
+    }
+
+    @Override
+    void onProcessComplete(TaskHandler handler, TraceRecord trace) {
+        println "I completed a task! It's name is '${handler.task.name}'"
+    }
+
+    @Override
+    void onProcessCached(TaskHandler handler, TraceRecord trace) {
+        println "I found a task in the cache! It's name is '${handler.task.name}'"
+    }
+
+    @Override
+    void onFilePublish(Path destination, Path source) {
+        println "I published a file! It's located at ${path.toUriString()}"
+    }
+    
+    @Override
+    void onFlowError(TaskHandler handler, TraceRecord trace) {
+        println "Uh oh, something went wrong..."
+    }
+
+    @Override
+    void onFlowComplete() {
+        println 'All done!'
+    }
+}
+```
+
+You can then use your trace observer by simply enabling the plugin in your pipeline. In the above example, the observer must also be enabled with a config option:
+
+```groovy
+myplugin.enabled = true
 ```
 
-## Plugin releases
+Refer to the `TraceObserver` [source code](https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/trace/TraceObserver.groovy) for descriptions of the available workflow events.
+
+## Publishing plugins
+
+Nextflow resolves plugins through a plugin registry, which stores metadata for each plugin version, including the publishing date, checksum, and download URL for the plugin binary. The default registry is located on GitHub at [nextflow-io/plugins](https://github.com/nextflow-io/plugins/), specifically [this file](https://raw.githubusercontent.com/nextflow-io/plugins/main/plugins.json).
 
-A plugin release is a ZIP archive containing the plugin classes and the required dependencies.
+To publish a plugin, you must create the plugin release, publish it to GitHub, and make a pull request against the main plugin registry with the metadata for your plugin release.
+
+A plugin release is a ZIP archive containing the compiled plugin classes, the required dependencies, and a JSON file with the plugin metadata. See the [`nf-hello`](https://github.com/nextflow-io/nf-hello) example to see how to create a plugin release.
+
+Here is an example meta file for a plugin release:
+
+```json
+{
+    "version": "0.2.0",
+    "url": "https://github.com/nextflow-io/nf-amazon/releases/download/0.2.0/nf-amazon-0.2.0.zip",
+    "date": "2020-10-12T10:05:44.28+02:00",
+    "sha512sum": "9e9e33695c1a7c051271..."
+}
+```
 
-Nextflow core plugins are released under a corresponding GitHub project, e.g. `nextflow-io/nf-amazon`. This is not a strict requirement, rather it is done to simplify the build process and provide a consistent download experience.
+(testing-plugins)=
 
-### Installation
+## Testing plugins
 
 Plugins must be declared in the `nextflow.config` file using the `plugins` scope, for example:
 
@@ -94,8 +374,48 @@ Since each Nextflow run can have a different set of plugins (and versions), each
 
 Additionally, the "default plugins" (defined in the Nextflow resources file `modules/nextflow/src/main/resources/META-INF/plugins-info.txt`) are always made available for use. To disable the use of default plugins, set the environment variable `NXF_PLUGINS_DEFAULT=false`.
 
+When running in development mode, the plugin system uses the `DevPluginClasspath` to load plugin classes from each plugin project build path, e.g. `plugins/nf-amazon/build/classes` and `plugins/nf-amazon/build/target/libs` (for deps libraries).
+
+## Environment variables
+
+The following environment variables are available when developing and testing plugins:
+
+`NXF_PLUGINS_MODE`
+: The plugin execution mode, either `prod` for production or `dev` for development (see below for details).
+
+`NXF_PLUGINS_DIR`
+: The path where the plugin archives are loaded and stored (default: `$NXF_HOME/plugins` in production, `./plugins` in development).
+
+`NXF_PLUGINS_DEFAULT`
+: Whether to use the default plugins when no plugins are specified in the Nextflow configuration (default: `true`).
+
+`NXF_PLUGINS_DEV`
+: Comma-separated list of development plugin root directories.
+
+`NXF_PLUGINS_TEST_REPOSITORY`
+: :::{versionadded} 23.04.0
+  :::
+: Comma-separated list of URIs for additional plugin registries or meta files, which will be used in addition to the default registry.
+: The URI should refer to a plugins repository JSON file or a specific plugin JSON meta file. In the latter case it should match the pattern `https://host.name/some/path/<plugin id>-X.Y.Z-meta.json`.
+
+: For example:
+
+    ```bash
+    # custom plugin repository at https://github.com/my-org/plugins
+    export NXF_PLUGINS_TEST_REPOSITORY="https://raw.githubusercontent.com/my-org/plugins/main/plugins.json"
+
+    # custom plugin release
+    export NXF_PLUGINS_TEST_REPOSITORY="https://github.com/nextflow-io/nf-hello/releases/download/0.3.0/nf-hello-0.3.0-meta.json"
+
+    nextflow run <pipeline> -plugins nf-hello
+    ```
+
+: This variable is useful for testing a plugin release before publishing it to the main registry.
+
 ## Gradle Tasks
 
+The following build tasks are defined in the `build.gradle` of each core plugin as well as the `nf-hello` example plugin.
+
 ### `makeZip`
 
 Create the plugin archive and JSON meta file in the subproject `build/libs` directory.
diff --git a/docs/dsl1.md b/docs/dsl1.md
index 50cea72d4e..04b82fec76 100644
--- a/docs/dsl1.md
+++ b/docs/dsl1.md
@@ -6,7 +6,7 @@ In Nextflow version `22.03.0-edge`, DSL2 became the default DSL version. In vers
 
 In Nextflow versions prior to `22.03.0-edge`, you must enable DSL2 explicitly in order to use it. You can either set the feature flag in your pipeline script:
 
-```groovy
+```nextflow
 nextflow.enable.dsl=2
 ```
 
@@ -20,7 +20,7 @@ export NXF_DEFAULT_DSL=2
 
 In DSL1, a process definition is also the process invocation. Process inputs and outputs are connected to channels using `from` and `into`. Here is the {ref}`your-first-script` example written in DSL1:
 
-```groovy
+```nextflow
 nextflow.enable.dsl=1
 
 params.str = 'Hello world!'
@@ -29,6 +29,7 @@ process splitLetters {
     output:
     file 'chunk_*' into letters
 
+    script:
     """
     printf '${params.str}' | split -b 6 - chunk_
     """
@@ -41,6 +42,7 @@ process convertToUpper {
     output:
     stdout result
 
+    script:
     """
     cat $x | tr '[a-z]' '[A-Z]'
     """
@@ -54,7 +56,7 @@ To migrate this code to DSL2, you need to move all of your channel logic through
 Refer to the {ref}`workflow-page` page to learn how to define a workflow. The DSL2 version of the above script is duplicated here for your convenience:
 
 ```{literalinclude} snippets/your-first-script.nf
-:language: groovy
+:language: nextflow
 ```
 
 ## Channel forking
@@ -65,7 +67,7 @@ In DSL2, channels are automatically forked when connecting two or more consumers
 
 For example, this would not work in DSL1 but is not a problem in DSL2:
 
-```groovy
+```nextflow
 Channel
     .from('Hello','Hola','Ciao')
     .set{ cheers }
@@ -88,7 +90,7 @@ In DSL1, the entire Nextflow pipeline must be defined in a single file (e.g. `ma
 DSL2 introduces the concept of "module scripts" (or "modules" for short), which are Nextflow scripts that can be "included" by other scripts. While modules are not essential to migrating to DSL2, nor are they mandatory in DSL2 by any means, modules can help you organize a large pipeline into multiple smaller files, and take advantage of modules created by others. Check out the {ref}`module-page` to get started.
 
 :::{note}
-With DSL2, the Groovy shell used by Nextflow also imposes a 64KB size limit on pipeline scripts, so if your DSL1 script is very large, you may need to split your script into modules anyway to avoid this limit.
+DSL2 scripts cannot exceed 64 KB in size. Large DSL1 scripts may need to be split into modules to avoid this limit.
 :::
 
 ## Deprecations
@@ -105,7 +107,7 @@ With DSL2, the Groovy shell used by Nextflow also imposes a 64KB size limit on p
 
   For example:
 
-  ```groovy
+  ```nextflow
   process foo {
       input:
       tuple X, 'some-file.sam'
@@ -121,7 +123,7 @@ With DSL2, the Groovy shell used by Nextflow also imposes a 64KB size limit on p
 
   Use:
 
-  ```groovy
+  ```nextflow
   process foo {
       input:
       tuple val(X), path('some-file.sam')
@@ -164,7 +166,7 @@ An early preview of DSL2 was available in 2020. Note that some of that early DSL
 
   For example:
 
-  ```groovy
+  ```nextflow
   include './some/library'
   include bar from './other/library'
 
@@ -176,7 +178,7 @@ An early preview of DSL2 was available in 2020. Note that some of that early DSL
 
   Should be replaced with:
 
-  ```groovy
+  ```nextflow
   include { foo } from './some/library'
   include { bar } from './other/library'
 
diff --git a/docs/executor.md b/docs/executor.md
index ab1febff8a..ec77c89254 100644
--- a/docs/executor.md
+++ b/docs/executor.md
@@ -95,7 +95,7 @@ Resource requests and other job characteristics can be controlled via the follow
 
 The `flux` executor allows you to run your pipeline script using the [Flux Framework](https://flux-framework.org).
 
-Nextflow manages each process as a separate job that is submitted to the cluster by using the `flux mini submit` command.
+Nextflow submits each process to the cluster as a separate job using the `flux submit` command.
 
 To enable the Flux executor, set `process.executor = 'flux'` in the `nextflow.config` file.
 
@@ -252,10 +252,22 @@ The `local` executor is used by default. It runs the pipeline processes on the c
 
 The `local` executor is useful for developing and testing a pipeline script on your computer, before switching to a cluster or cloud environment with production data.
 
+Resource requests and other job characteristics can be controlled via the following process directives:
+
+- {ref}`process-cpus`
+- {ref}`process-memory`
+- {ref}`process-time`
+- {ref}`process-container`
+- {ref}`process-containerOptions`
+
 :::{note}
 While the `local` executor limits the number of concurrent tasks based on requested vs available resources, it does not enforce task resource requests. In other words, it is possible for a local task to use more CPUs and memory than it requested, in which case it may starve other tasks. An exception to this behavior is when using {ref}`container-docker` or {ref}`container-podman` containers, in which case the resource requests are enforced by the container runtime.
 :::
 
+The local executor supports two types of tasks:
+- Script tasks (processes with a `script` or `shell` block) - executed via a Bash wrapper
+- Native tasks (processes with an `exec` block) - executed directly in the JVM.
+
 (lsf-executor)=
 
 ## LSF
diff --git a/docs/flux.md b/docs/flux.md
index 6e16ac103b..8d72ce4971 100644
--- a/docs/flux.md
+++ b/docs/flux.md
@@ -1,6 +1,6 @@
 (flux-page)=
 
-# Flux Framework
+# Using Nextflow with Flux
 
 :::{versionadded} 22.11.0-edge
 :::
@@ -36,9 +36,9 @@ For additional Flux settings, see the {ref}`flux-executor` section.
 
 Here is an example pipeline that we will use:
 
-```groovy
+```nextflow
 workflow {
-    breakfast = Channel.from '🥞️', '🥑️', '🥧️', '🍵️', '🍞️'
+    breakfast = Channel.of '🥞️', '🥑️', '🥧️', '🍵️', '🍞️'
     haveMeal(breakfast)
 }
 
@@ -100,7 +100,7 @@ Here is an example of submitting a job and getting the log for it.
 First submit the job:
 
 ```console
-$ flux mini submit echo "HELLO MOTO"
+$ flux submit echo "HELLO MOTO"
 ƒEzWqspb
 ```
 
@@ -114,7 +114,7 @@ HELLO MOTO
 Try submitting a longer job:
 
 ```console
-$ flux mini submit sleep 60
+$ flux submit sleep 60
 ```
 
 And then seeing it in the jobs listing.
diff --git a/docs/fusion.md b/docs/fusion.md
index 95cb14d33d..bf15304522 100644
--- a/docs/fusion.md
+++ b/docs/fusion.md
@@ -44,7 +44,7 @@ configuration. For example:
 fusion.enabled = true
 wave.enabled = true
 process.executor = 'azure-batch'
-tower.accessToken = '<your platform access token>'
+tower.accessToken = '<your platform access token>' // optional
 ```
 
 Then run your pipeline using the usual command:
@@ -71,7 +71,7 @@ wave.enabled = true
 process.executor = 'awsbatch'
 process.queue = '<YOUR BATCH QUEUE>'
 aws.region = '<YOUR AWS REGION>'
-tower.accessToken = '<your platform access token>'
+tower.accessToken = '<your platform access token>' // optional
 ```
 
 Then you can run your pipeline using the following command:
@@ -146,7 +146,7 @@ configuration. For example:
 fusion.enabled = true
 wave.enabled = true
 process.executor = 'google-batch'
-tower.accessToken = '<your platform access token>'
+tower.accessToken = '<your platform access token>' // optional
 ```
 
 Then run your pipeline using the usual command:
@@ -172,10 +172,10 @@ process.executor = 'k8s'
 k8s.context = '<YOUR K8S CONFIGURATION CONTEXT>'
 k8s.namespace = '<YOUR K8S NAMESPACE>'
 k8s.serviceAccount = '<YOUR K8S SERVICE ACCOUNT>'
-tower.accessToken = '<your platform access token>'
+tower.accessToken = '<your platform access token>' // optional
 ```
 
-The `k8s.context` represents the Kubernetes configuration context to be used for the pipeline execution. This setting can be omitted if Nextflow itself is run as a pod in the Kubernetes clusters.
+The `k8s.context` represents the Kubernetes configuration context to be used for the pipeline execution. This setting can be omitted if Nextflow itself is running as a pod in the Kubernetes clusters.
 
 The `k8s.namespace` represents the Kubernetes namespace where the jobs submitted by the pipeline execution should be executed.
 
@@ -191,9 +191,10 @@ nextflow run <YOUR PIPELINE> -work-dir s3://<YOUR BUCKET>/scratch
 You an also use Fusion and Kubernetes with Azure Blob Storage and Google Storage using the same deployment approach.
 :::
 
-### Local execution
+### Local execution with AWS S3
 
-Fusion file system allows the use of an S3 bucket as a pipeline work directory with the Nextflow local executor. This configuration requires the use of Docker (or similar container engine) for the execution of your pipeline tasks.
+Fusion file system allows the use of an S3 bucket as a pipeline work directory with the Nextflow local executor. This
+configuration requires the use of Docker (or similar container engine) for the execution of your pipeline tasks.
 
 The AWS S3 bucket credentials should be made accessible via standard `AWS_ACCESS_KEY_ID` and `AWS_SECRET_ACCESS_KEY` environment variables.
 
@@ -204,6 +205,7 @@ docker.enabled = true
 fusion.enabled = true
 fusion.exportStorageCredentials = true
 wave.enabled = true
+tower.accessToken = '<your platform access token>' // optional
 ```
 
 Then you can run your pipeline using the following command:
@@ -212,7 +214,7 @@ Then you can run your pipeline using the following command:
 nextflow run <YOUR PIPELINE> -work-dir s3://<YOUR BUCKET>/scratch
 ```
 
-Replace `<YOUR PIPELINE>` and `<YOUR BUCKET>` with a pipeline script and bucket or your choice, for example:
+Replace `<YOUR PIPELINE>` and `<YOUR BUCKET>` with a pipeline script and bucket of your choice, for example:
 
 ```bash
 nextflow run https://github.com/nextflow-io/rnaseq-nf -work-dir s3://nextflow-ci/scratch
@@ -220,7 +222,98 @@ nextflow run https://github.com/nextflow-io/rnaseq-nf -work-dir s3://nextflow-ci
 
 :::{warning}
 The option `fusion.exportStorageCredentials` leaks the AWS credentials on the task launcher script created by Nextflow.
-This option should only be used for development purposes.
+This option should only be used for testing and development purposes.
+:::
+
+### Local execution with Minio
+
+[Minio](https://min.io/) is an open source, enterprise grade, object storage compatible with AWS S3. Nextflow and Fusion
+can use Minio (or other S3-compatible object storages) as an alternative to AWS S3 in some deployment scenarios.
+
+This configuration requires the the use of Nextflow local execution and Docker (or similar container engine) for the
+execution of your pipeline tasks.
+
+For the same of this example, runs a local instance of Minio using this command:
+
+```
+docker run -p 9000:9000 \
+    --rm -d -p 9001:9001 \
+    -e "MINIO_ROOT_USER=admin" \
+    -e "MINIO_ROOT_PASSWORD=secret" \
+    quay.io/minio/minio server /data --console-address ":9001"
+```
+
+Open the Minio console opening in your browser this address `http://localhost:9001`, then create a credentials pair,
+and a bucket. For the sake of this example the bucket name `foobar` will be used.
+
+
+The following configuration should be added in your Nextflow configuration file:
+
+```groovy
+aws.accessKey = '<YOUR MINIO ACCESS KEY>'
+aws.secretKey = '<YOUR MINIO SECRET KEY>'
+aws.client.endpoint = 'http://localhost:9000'
+aws.client.s3PathStyleAccess = true
+wave.enabled = true
+fusion.enabled = true
+fusion.exportStorageCredentials = true
+docker.enabled = true
+tower.accessToken = '<your platform access token>' // optional
+```
+
+Then you can run your pipeline using the following command:
+
+```bash
+nextflow run <YOUR PIPELINE> -work-dir s3://foobar/scratch
+```
+
+Replace `<YOUR PIPELINE>` with a pipeline script and bucket of your choice:
+
+:::{warning}
+The option `fusion.exportStorageCredentials` leaks the AWS credentials on the task launcher script created by Nextflow.
+This option should only be used for testing and development purposes.
+:::
+
+### Local execution with Oracle Object Storage
+
+Fusion file system and Nextflow are compatible with [Oracle Object Storage](https://www.oracle.com/cloud/storage/object-storage/).
+
+:::{note}
+This capability relies on the S3-like API compatibility provided by Oracle storage and not by a native support in
+Nextflow and Fusion. As such it may not fully work and support all Nextflow and Fusion features.
+:::
+
+This configuration requires the execution of your pipeline tasks using Docker or a similar container engine.
+
+The following should be included in your Nextflow configuration file:
+
+```groovy
+aws.region = '<YOUR_REGION>'
+aws.accessKey = '<YOUR_ACCESS_KEY>'
+aws.secretKey = '<YOUR_SECRET_KEY>'
+aws.client.endpoint = 'https://<YOUR_BUCKET_NAMESPACE>.compat.objectstorage.<YOUR_REGION>.oraclecloud.com'
+aws.client.s3PathStyleAccess = true
+aws.client.protocol = 'https'
+aws.client.signerOverride = 'AWSS3V4SignerType'
+docker.enabled = true
+docker.containerOptions = '-e FUSION_AWS_REGION=<YOUR_REGION>'
+fusion.enabled = true
+fusion.exportStorageCredentials = true
+wave.enabled = true
+tower.accessToken = '<YOUR_PLATFORM_ACCESS_TOKEN>' // optional
+```
+
+Then you can run your pipeline using the following command:
+
+```bash
+nextflow run <YOUR_PIPELINE> -work-dir s3://<YOUR_BUCKET>/scratch
+```
+
+In the above snippet replace the placeholders `<YOUR_ACCESS_KEY>` and `<YOUR_SECRET_KEY>` with your [Oracle Customer Secret Key](https://docs.oracle.com/en-us/iaas/Content/Identity/Tasks/managingcredentials.htm#Working2),
+and the placeholders `<YOUR_BUCKET_NAMESPACE>` and `<YOUR_REGION>` with the namespace and region of your Oracle bucket.
+
+:::{warning}
+The `fusion.exportStorageCredentials` option leaks the Oracle credentials to the Nextflow task launcher script and should only be used for testing and development purposes.
 :::
 
 ## Advanced settings
diff --git a/docs/git.md b/docs/git.md
new file mode 100644
index 0000000000..fbb5f4ef83
--- /dev/null
+++ b/docs/git.md
@@ -0,0 +1,241 @@
+(git-page)=
+
+# Git
+
+## Git configuration
+
+The file `$HOME/.nextflow/scm` allows you to centralise the security credentials required to access private project repositories on Bitbucket, GitHub and GitLab source code management (SCM) platforms or to manage the configuration properties of private server installations (of the same platforms).
+
+The configuration properties for each Git provider are defined inside the `providers` section. Properties for the same provider are grouped with a common name and delimited with curly brackets. For example:
+
+```groovy
+providers {
+    <provider-name> {
+        property = value
+        // ...
+    }
+}
+```
+
+In the above template replace `<provider-name>` with one of the "default" servers (i.e. `bitbucket`, `github` or `gitlab`) or a custom identifier representing a private SCM server installation.
+
+:::{versionadded} 20.10.0
+A custom location for the SCM file can be specified using the `NXF_SCM_FILE` environment variable.
+:::
+
+The following configuration properties are supported for each provider configuration:
+
+`providers.<provider>.user`
+: User name required to access private repositories on the SCM server.
+
+`providers.<provider>.password`
+: User password required to access private repositories on the SCM server.
+
+`providers.<provider>.token`
+: *Required only for private Gitlab servers*
+: Private API access token.
+
+`providers.<provider>.platform`
+: *Required only for private SCM servers*
+: Git provider name, either: `github`, `gitlab` or `bitbucket`.
+
+`providers.<provider>.server`
+: *Required only for private SCM servers*
+: SCM server name including the protocol prefix e.g. `https://github.com`.
+
+`providers.<provider>.endpoint`
+: *Required only for private SCM servers*
+: SCM API `endpoint` URL e.g. `https://api.github.com` (default: the same as `providers.<provider>.server`).
+
+## Git providers
+
+### BitBucket
+
+Create a `bitbucket` entry in the [SCM configuration file](#git-configuration) specifying your user name and app password, as shown below:
+
+```groovy
+providers {
+    bitbucket {
+        user = 'me'
+        password = 'my-secret'
+    }
+}
+```
+
+:::{note}
+App passwords are substitute passwords for a user account which you can use for scripts and integrating tools in order to avoid putting your real password into configuration files. Learn more at [this link](https://support.atlassian.com/bitbucket-cloud/docs/app-passwords/).
+:::
+
+### BitBucket Server
+
+[BitBucket Server](https://confluence.atlassian.com/bitbucketserver) is a self-hosted Git repository and management platform.
+
+:::{note}
+BitBucket Server uses a different API from the [BitBucket](https://bitbucket.org/) Cloud service. Make sure to use the right configuration whether you are using the cloud service or a self-hosted installation.
+:::
+
+To access your local BitBucket Server create an entry in the [SCM configuration file](#git-configuration) specifying as shown below:
+
+```groovy
+providers {
+    mybitbucket {
+        platform = 'bitbucketserver'
+        server = 'https://your.bitbucket.host.com'
+        endpoint = 'https://your.bitbucket.host.com'
+        user = 'your-user'
+        password = 'your-password or your-token'
+    }
+}
+```
+
+### GitHub
+
+Create a `github` entry in the [SCM configuration file](#git-configuration) specifying your user name and access token as shown below:
+
+```groovy
+providers {
+    github {
+        user = 'your-user-name'
+        password = 'your-personal-access-token'
+    }
+}
+```
+
+GitHub requires the use of a personal access token (PAT) in place of a password when accessing APIs. Learn more about PAT and how to create it at [this link](https://docs.github.com/en/github/authenticating-to-github/keeping-your-account-and-data-secure/creating-a-personal-access-token).
+
+:::{versionadded} 23.01.0-edge
+Nextflow automatically uses the `GITHUB_TOKEN` environment variable to authenticate access to the GitHub repository if no credentials are provided via the `scm` file. This is useful especially when accessing pipeline code from a GitHub Action. Read more about the token authentication in the [GitHub documentation](https://docs.github.com/en/actions/security-guides/automatic-token-authentication).
+:::
+
+### GitLab
+
+Create a `gitlab` entry in the [SCM configuration file](#git-configuration) specifying the user name, password and your API access token that can be found in your GitLab [account page](https://gitlab.com/profile/account) (sign in required). For example:
+
+```groovy
+providers {
+    gitlab {
+        user = 'me'
+        password = 'my-secret'
+        token = 'YgpR8m7viH_ZYnC8YSe8'
+    }
+}
+```
+
+:::{tip}
+The GitLab *token* string can be used as the `password` value in the above setting. When doing that the `token` field can be omitted.
+:::
+
+### Gitea
+
+[Gitea](https://gitea.io) is a Git repository server with GitHub-like GUI access. Since Gitea installation is quite easy, it is suitable for building a private development environment in your network. To access your Gitea server, you have to provide all the credential information below:
+
+```groovy
+providers {
+    mygitea {
+        server = 'http://your-domain.org/gitea'
+        endpoint = 'http://your-domain.org/gitea/api/v1'
+        platform = 'gitea'
+        user = 'your-user'
+        password = 'your-password'
+        token = 'your-api-token'
+    }
+}
+```
+
+See [Gitea documentation](https://docs.gitea.io/en-us/api-usage/) about how to enable API access on your server and how to issue a token.
+
+### Azure Repos
+
+Nextflow has builtin support for [Azure Repos](https://azure.microsoft.com/en-us/services/devops/repos/), a Git source code management service hosted in the Azure cloud. To access your Azure Repos with Nextflow provide the repository credentials using the configuration snippet shown below:
+
+```groovy
+providers {
+    azurerepos {
+        user = 'your-user-name'
+        password = 'your-personal-access-token'
+    }
+}
+```
+
+:::{tip}
+The Personal access token can be generated in the repository `Clone Repository` dialog.
+:::
+
+(aws-codecommit)=
+
+### AWS CodeCommit
+
+:::{versionadded} 22.06.0-edge
+:::
+
+Nextflow supports [AWS CodeCommit](https://aws.amazon.com/codecommit/) as a Git provider to access and to share pipelines code.
+
+To access your project hosted on AWS CodeCommit with Nextflow provide the repository credentials using the configuration snippet shown below:
+
+```groovy
+providers {
+    my_aws_repo {
+        platform = 'codecommit'
+        user = '<AWS ACCESS KEY>'
+        password = '<AWS SECRET KEY>'
+    }
+}
+```
+
+In the above snippet replace `<AWS ACCESS KEY>` and `<AWS SECRET KEY>` with your AWS credentials, and `my_aws_repo` with a name of your choice.
+
+:::{tip}
+The `user` and `password` settings are optional. If omitted, the [AWS default credentials provider chain](https://docs.aws.amazon.com/sdk-for-java/v1/developer-guide/credentials.html) is used.
+:::
+
+Then the pipeline can be accessed with Nextflow as shown below:
+
+```bash
+nextflow run https://git-codecommit.eu-west-1.amazonaws.com/v1/repos/my-repo
+```
+
+In the above example replace `my-repo` with your own repository. Note also that AWS CodeCommit has different URLs depending the region in which you are working.
+
+:::{note}
+The support for protocols other than HTTPS is not available at this time.
+:::
+
+## Private server configuration
+
+Nextflow is able to access repositories hosted on private BitBucket, GitHub, GitLab and Gitea server installations.
+
+In order to use a private SCM installation you will need to set the server name and access credentials in your [SCM configuration file](#git-configuration) .
+
+If, for example, the host name of your private GitLab server is `gitlab.acme.org`, you will need to have in the `$HOME/.nextflow/scm` file a configuration like the following:
+
+```groovy
+providers {
+    mygit {
+        server = 'http://gitlab.acme.org'
+        platform = 'gitlab'
+        user = 'your-user'
+        password = 'your-password'
+        token = 'your-api-token'
+    }
+}
+```
+
+Then you will be able to run/pull a project with Nextflow using the following command line:
+
+```bash
+nextflow run foo/bar -hub mygit
+```
+
+Or, alternatively, using the Git clone URL:
+
+```bash
+nextflow run http://gitlab.acme.org/foo/bar.git
+```
+
+:::{note}
+You must also specify the server API endpoint URL if it differs from the server base URL. For example, for GitHub Enterprise V3, add `endpoint = 'https://git.your-domain.com/api/v3'`.
+:::
+
+:::{warning}
+When accessing a private SCM installation over `https` from a server that uses a custom SSL certificate, you may need to import the certificate into your local Java keystore. See [Import the Certificate as a Trusted Certificate](https://docs.oracle.com/javase/tutorial/security/toolsign/rstep2.html) for more information.
+:::
diff --git a/docs/google.md b/docs/google.md
index 232fcc29fd..703948c103 100644
--- a/docs/google.md
+++ b/docs/google.md
@@ -99,11 +99,12 @@ location and that fits the requested resources. If `memory` is not specified, 1
 The `machineType` directive can be used to request a specific VM instance type. It can be any predefined Google Compute
 Platform [machine type](https://cloud.google.com/compute/docs/machine-types) or [custom machine type](https://cloud.google.com/compute/docs/instances/creating-instance-with-custom-machine-type).
 
-```groovy
+```nextflow
 process myTask {
     cpus 8
     memory '40 GB'
 
+    script:
     """
     your_command --here
     """
@@ -112,6 +113,7 @@ process myTask {
 process anotherTask {
     machineType 'n1-highmem-8'
 
+    script:
     """
     your_command --here
     """
@@ -124,12 +126,13 @@ process anotherTask {
 The `machineType` directive can also be a comma-separated list of patterns. The pattern can contain a `*` to match any
 number of characters and `?` to match any single character. Examples of valid patterns: `c2-*`, `m?-standard*`, `n*`.
 
-```groovy
+```nextflow
 process myTask {
     cpus 8
     memory '20 GB'
     machineType 'n2-*,c2-*,m3-*'
 
+    script:
     """
     your_command --here
     """
@@ -142,12 +145,13 @@ process myTask {
 The `machineType` directive can also be an [Instance Template](https://cloud.google.com/compute/docs/instance-templates),
 specified as `template://<instance-template>`. For example:
 
-```groovy
+```nextflow
 process myTask {
     cpus 8
     memory '20 GB'
     machineType 'template://my-template'
 
+    script:
     """
     your_command --here
     """
@@ -156,7 +160,7 @@ process myTask {
 
 :::{note}
 Using an instance template will overwrite the `accelerator` and `disk` directives, as well as the following Google Batch
-config options: `cpuPlatform`, `preemptible`, and `spot`.
+config options: `bootDiskImage`, `cpuPlatform`, `preemptible`, and `spot`.
 :::
 
 To use an instance template with GPUs, you must also set the `google.batch.installGpuDrivers` config option to `true`.
@@ -172,7 +176,7 @@ The `disk` directive can be used to set the boot disk size or provision a disk f
 
 Examples:
 
-```groovy
+```nextflow
 // set the boot disk size
 disk 100.GB
 
@@ -335,22 +339,24 @@ The process `machineType` directive may optionally be used to specify a predefin
 
 Examples:
 
-```groovy
+```nextflow
 process custom_resources_task {
     cpus 8
     memory '40 GB'
     disk '200 GB'
 
+    script:
     """
-    <Your script here>
+    your_command --here
     """
 }
 
 process predefined_resources_task {
     machineType 'n1-highmem-8'
 
+    script:
     """
-    <Your script here>
+    your_command --here
     """
 }
 ```
@@ -398,25 +404,26 @@ For an exhaustive list of error codes, refer to the official Google Life Science
 
 ### Hybrid execution
 
-Nextflow allows the use of multiple executors in the same workflow. This feature enables the deployment of hybrid workloads, in which some jobs are executed in the local computer or local computing cluster, and some jobs are offloaded to Google Life Sciences.
+Nextflow allows the use of multiple executors in the same workflow. This feature enables the deployment of hybrid workloads, in which some jobs are executed in the local computer or local computing cluster, and some jobs are offloaded to Google Cloud (either Google Batch or Google Life Sciences).
 
-To enable this feature, use one or more {ref}`config-process-selectors` in your Nextflow configuration file to apply the Google Life Sciences executor to the subset of processes that you want to offload. For example:
+To enable this feature, use one or more {ref}`config-process-selectors` in your Nextflow configuration file to apply the Google Cloud executor to the subset of processes that you want to offload. For example:
 
 ```groovy
 process {
     withLabel: bigTask {
-        executor = 'google-lifesciences'
+        executor = 'google-batch' // or 'google-lifesciences'
         container = 'my/image:tag'
     }
 }
 
 google {
     project = 'your-project-id'
-    zone = 'europe-west1-b'
+    location = 'us-central1' // for Google Batch
+    // zone = 'us-central1-a' // for Google Life Sciences
 }
 ```
 
-Then launch the pipeline with the `-bucket-dir` option to specify a Google Storage path for the jobs computed with Google Life Sciences and, optionally, the `-work-dir` to specify the local storage for the jobs computed locally:
+Then launch the pipeline with the `-bucket-dir` option to specify a Google Storage path for the jobs computed with Google Cloud and, optionally, the `-work-dir` to specify the local storage for the jobs computed locally:
 
 ```bash
 nextflow run <script or project name> -bucket-dir gs://my-bucket/some/path
@@ -426,6 +433,10 @@ nextflow run <script or project name> -bucket-dir gs://my-bucket/some/path
 The Google Storage path needs to contain at least one sub-directory (e.g. `gs://my-bucket/work` rather than `gs://my-bucket`).
 :::
 
+:::{note}
+Nextflow will automatically manage the transfer of input and output files between the local and cloud environments when using hybrid workloads.
+:::
+
 ### Limitations
 
 - Compute resources in Google Cloud are subject to [resource quotas](https://cloud.google.com/compute/quotas), which may affect your ability to run pipelines at scale. You can request quota increases, and your quotas may automatically increase over time as you use the platform. In particular, GPU quotas are initially set to 0, so you must explicitly request a quota increase in order to use GPUs. You can initially request an increase to 1 GPU at a time, and after one billing cycle you may be able to increase it further.
diff --git a/docs/index.md b/docs/index.md
index 69476d91c7..f1585124d4 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -53,34 +53,33 @@ your-first-script
 
 ```{toctree}
 :hidden:
-:caption: Language
+:caption: Running pipelines
 :maxdepth: 1
 
-script
-process
-channel
-operator
-workflow
-module
+cli
 config
-dsl1
+executor
+cache-and-resume
+reports
+plugins
 ```
 
 ```{toctree}
 :hidden:
-:caption: Execution
+:caption: Developing pipelines
 :maxdepth: 1
 
-cli
-executor
-cache-and-resume
-tracing
-metrics
-sharing
-metadata
-mail
-plugins
+script
+working-with-files
+process
+channel
+workflow
+module
+notifications
 secrets
+sharing
+vscode
+dsl1
 ```
 
 ```{toctree}
@@ -88,6 +87,7 @@ secrets
 :caption: Software dependencies
 :maxdepth: 1
 
+git
 container
 conda
 spack
@@ -96,23 +96,31 @@ wave
 
 ```{toctree}
 :hidden:
-:caption: Compute & storage platforms
+:caption: Compute & storage
 :maxdepth: 1
 
 aws
 amazons3
 azure
-fusion
 google
 kubernetes
+fusion
 ```
 
 ```{toctree}
 :hidden:
-:caption: Additional integrations
+:caption: Reference
 :maxdepth: 1
 
-flux
+reference/syntax
+reference/cli
+reference/config
+reference/env-vars
+reference/feature-flags
+reference/stdlib
+reference/process
+reference/channel
+reference/operator
 ```
 
 ```{toctree}
@@ -125,3 +133,12 @@ developer/diagram
 developer/packages
 developer/plugins
 ```
+
+```{toctree}
+:hidden:
+:caption: Tutorials
+:maxdepth: 1
+
+flux
+metrics
+```
diff --git a/docs/install.md b/docs/install.md
index a55c68445a..246ce57fcb 100644
--- a/docs/install.md
+++ b/docs/install.md
@@ -6,12 +6,16 @@
 
 ## Requirements
 
-Nextflow can be used on any POSIX-compatible system (Linux, macOS, etc), and on Windows through [WSL](https://en.wikipedia.org/wiki/Windows_Subsystem_for_Linux). It requires Bash 3.2 (or later) and [Java 11 (or later, up to 22)](http://www.oracle.com/technetwork/java/javase/downloads/index.html) to be installed. You can see which version you have using the following command:
+Nextflow can be used on any POSIX-compatible system (Linux, macOS, etc), and on Windows through [WSL](https://en.wikipedia.org/wiki/Windows_Subsystem_for_Linux). It requires Bash 3.2 (or later) and [Java 17 (or later, up to 23)](http://www.oracle.com/technetwork/java/javase/downloads/index.html) to be installed. You can see which version you have using the following command:
 
 ```bash
 java -version
 ```
 
+:::{versionchanged} 24.11.0-edge
+Support for Java versions prior to 17 was dropped.
+:::
+
 If you don't have a compatible version of Java installed in your computer, it is recommended that you install it through [SDKMAN!](https://sdkman.io/), and that you use the latest LTS version of Temurin. See [this website](https://whichjdk.com/) for more information.
 
 To install Java with SDKMAN:
@@ -60,12 +64,21 @@ Nextflow is distributed as a self-installing package, in order to make the insta
     chmod +x nextflow
     ```
 
-3. Move Nextflow into an executable path:
+3. Move Nextflow into an executable path. For example:
 
     ```bash
-    sudo mv nextflow /usr/local/bin
+    mkdir -p $HOME/.local/bin/
+    mv nextflow $HOME/.local/bin/
     ```
 
+    :::{tip}
+    Ensure the directory `$HOME/.local/bin/` is included in your `PATH` variable. Temporarily add this directory to `PATH` by setting `export PATH="$PATH:$HOME/.local/bin"`. Add the directory to `PATH` permanently by adding the export command to your shell configuration file, such as `~/.bashrc` or `~/.zshrc`. Alternatively, move the `nextflow` executable to a directory already in your `PATH`.
+    :::
+
+    :::{warning}
+    Nextflow will update its executable during the self update process, therefore the update can fail if the executable is placed in a directory with restricted permissions.
+    :::
+
 4. Confirm that Nextflow is installed correctly:
 
     ```bash
@@ -83,7 +96,7 @@ nextflow self-update
 You can also temporarily switch to a specific version of Nextflow with the `NXF_VER` environment variable. For example:
 
 ```bash
-NXF_VER=23.10.0 nextflow run hello
+NXF_VER=23.10.0 nextflow info
 ```
 
 ## Stable and edge releases
@@ -98,23 +111,33 @@ To use the latest edge release, set `NXF_EDGE=1` when updating:
 NXF_EDGE=1 nextflow self-update
 ```
 
-You can also use `NXF_VER` to switch to any edge release:
+You can also use `NXF_VER` to temporarily switch to any edge release. For example:
 
 ```bash
-$ nextflow info
+NXF_VER=24.06.0-edge nextflow info
 ```
 
 ## Standalone distribution
 
-Nextflow has a set of {ref}`core plugins <plugins-core>` which are downloaded at runtime by default. There is also a standalone distribution (i.e. the `all` distribution) which comes pre-packaged with all core plugins. This distribution is mainly useful for offline environments.
+The Nextflow standalone distribution (i.e. the `dist` distribution) consists of self-contained `nextflow` executable file
+that includes all the application dependencies for core functionalities, and it can run without downloading third parties
+libraries. This distribution is mainly useful for offline environments.
 
-The installer for the `all` distribution can be found on the [GitHub releases page](https://github.com/nextflow-io/nextflow/releases), under the "Assets" section for a specific release. The installation procedure is the same as for the standard distribution, only using this URL instead of `https://get.nextflow.io`:
+Note however the support for cloud services e.g. AWS, Seqera Platform, Wave, etc. still require the download
+of the corresponding Nextflow plugins.
 
-```bash
-export NXF_VER=23.10.0
-curl -s https://github.com/nextflow-io/nextflow/releases/download/v$NXF_VER/nextflow-$NXF_VER-all
-```
+To use the standalone distribution:
 
-:::{warning}
-The `all` distribution does not support third-party plugins. Only the {ref}`core plugins <plugins-core>` are supported.
-:::
+1. Download it from the [GitHub releases page](https://github.com/nextflow-io/nextflow/releases), under the "Assets" section for a specific
+
+2. Grant execution permissions to the downloaded file e.g.
+
+    ```
+    chmod -x nextflow-24.10.1-dist
+    ```
+
+3. Then you can use it as a drop-in replacement for `nextflow` command. For example:
+
+    ```
+    ./nextflow-24.10.1-dist run hello
+    ```
diff --git a/docs/metadata.md b/docs/metadata.md
deleted file mode 100644
index 2294e3cbe9..0000000000
--- a/docs/metadata.md
+++ /dev/null
@@ -1,225 +0,0 @@
-(metadata-page)=
-
-# Workflow introspection
-
-(metadata-workflow)=
-
-## Runtime metadata
-
-The implicit `workflow` object allows you to access some workflow and runtime metadata in your Nextflow scripts. For example:
-
-```groovy
-println "Project : $workflow.projectDir"
-println "Git info: $workflow.repository - $workflow.revision [$workflow.commitId]"
-println "Cmd line: $workflow.commandLine"
-println "Manifest's pipeline version: $workflow.manifest.version"
-```
-
-:::{tip}
-To shortcut access to multiple `workflow` properties, you can use the Groovy [with](<http://docs.groovy-lang.org/latest/html/groovy-jdk/java/lang/Object.html#with(groovy.lang.Closure)>) method.
-:::
-
-The following table lists the properties that can be accessed on the `workflow` object:
-
-
-`workflow.commandLine`
-: Command line as entered by the user to launch the workflow execution.
-
-`workflow.commitId`
-: Git commit ID of the executed workflow repository.
-: When providing a Git tag, branch name, or commit hash using the `-r` CLI option, the associated `workflow.commitId` is also populated.
-
-`workflow.complete`
-: *Available only in the `workflow.onComplete` handler*
-: Timestamp of workflow when execution is completed.
-
-`workflow.configFiles`
-: Configuration files used for the workflow execution.
-
-`workflow.container`
-: Docker image used to run workflow tasks. When more than one image is used it returns a map object containing `[process name, image name]` pair entries.
-
-`workflow.containerEngine`
-: Returns the name of the container engine (e.g. docker or singularity) or null if no container engine is enabled.
-
-`workflow.duration`
-: *Available only in the `workflow.onComplete` handler*
-: Time elapsed to complete workflow execution.
-
-`workflow.errorMessage`
-: *Available only in the `workflow.onComplete` and `workflow.onError` handlers*
-: Error message of the task that caused the workflow execution to fail.
-
-`workflow.errorReport`
-: *Available only in the `workflow.onComplete` and `workflow.onError` handlers*
-: Detailed error of the task that caused the workflow execution to fail.
-
-`workflow.exitStatus`
-: *Available only in the `workflow.onComplete` and `workflow.onError` handlers*
-: Exit status of the task that caused the workflow execution to fail.
-
-`workflow.failOnIgnore`
-: :::{versionadded} 24.05.0-edge
-  :::
-: Whether the `workflow.failOnIgnore` config option was enabled.
-
-: See {ref}`process-error-strategy` for use-cases of this option.
-
-`workflow.fusion.enabled`
-: Whether Fusion is enabled.
-
-`workflow.fusion.version`
-: Fusion version in use.
-
-`workflow.homeDir`
-: User system home directory.
-
-`workflow.launchDir`
-: Directory where the workflow execution has been launched.
-
-`workflow.manifest`
-: Entries of the workflow manifest.
-
-`workflow.preview`
-: :::{versionadded} 24.04.0
-  :::
-: Returns `true` whenever the current instance is a preview execution.
-
-`workflow.profile`
-: Used configuration profile.
-
-`workflow.projectDir`
-: Directory where the workflow project is stored in the computer.
-
-`workflow.repository`
-: Project repository Git remote URL.
-
-`workflow.resume`
-: Returns `true` whenever the current instance is resumed from a previous execution.
-
-`workflow.revision`
-: Git branch/tag of the executed workflow repository.
-: When providing a Git tag or branch name using the `-r` CLI option, the `workflow.revision` is also populated.
-
-`workflow.runName`
-: Mnemonic name assigned to this execution instance.
-
-`workflow.scriptFile`
-: Project main script file path.
-
-`workflow.scriptId`
-: Project main script unique hash ID.
-
-`workflow.scriptName`
-: Project main script file name.
-
-`workflow.sessionId`
-: Unique identifier (UUID) associated to current execution.
-
-`workflow.start`
-: Timestamp of workflow at execution start.
-
-`workflow.stubRun`
-: Returns `true` whenever the current instance is a stub-run execution .
-
-`workflow.success`
-: *Available only in the `workflow.onComplete` and `workflow.onError` handlers*
-: Reports if the execution completed successfully.
-
-`workflow.userName`
-: User system account name.
-
-`workflow.wave.enabled`
-: Whether Wave is enabled.
-
-`workflow.workDir`
-: Workflow working directory.
-
-(metadata-nextflow)=
-
-## Nextflow metadata
-
-The implicit `nextflow` object allows you to access the metadata information of the Nextflow runtime.
-
-`nextflow.build`
-: Nextflow runtime build number.
-
-`nextflow.timestamp`
-: Nextflow runtime compile timestamp.
-
-`nextflow.version`
-: Nextflow runtime version number.
-
-`nextflow.version.matches()`
-: Check whether the Nextflow runtime satisfies a version requirement.
-
-: The version requirement string can be prefixed with the usual comparison operators:
-  - `=` or `==`: equal to
-  - `<` (`<=`): less than (or equal to)
-  - `>` (`>=`): greater than (or equal to)
-  - `!=` or `<>`: not equal
-
-  For example:
-
-  ```groovy
-  if( !nextflow.version.matches('>=23.10') ) {
-      error "This workflow requires Nextflow version 23.10 or greater -- You are running version $nextflow.version"
-  }
-  ```
-
-: Alternatively, the version can be postfixed with `+`, which is similar to `==` but also allows the last version part to be greater. For example, `23.10.1+` is satisfied by `23.10.1` and `23.10.2`, but not `23.11.x` or `23.09.x`. Additionally, `23.10.+` is equivalent to `23.10.0+`. This operator is a useful way to enforce a specific version while allowing for newer patch releases.
-
-(metadata-completion-handler)=
-
-## Completion handler
-
-Due to the asynchronous nature of Nextflow the termination of a script does not correspond to the termination of the running workflow. Thus some information, only available on execution completion, needs to be accessed by using an asynchronous handler.
-
-The `onComplete` event handler is invoked by the framework when the workflow execution is completed. It allows one to access the workflow termination status and other useful information. For example:
-
-```groovy
-workflow.onComplete {
-    println "Pipeline completed at: $workflow.complete"
-    println "Execution status: ${ workflow.success ? 'OK' : 'failed' }"
-}
-```
-
-If you want an e-mail notification on completion, check {ref}`mail-page`.
-
-(metadata-error-handler)=
-
-## Error handler
-
-The `onError` event handler is invoked by Nextflow when a runtime or process error caused the pipeline execution to stop. For example:
-
-```groovy
-workflow.onError {
-    println "Error: Pipeline execution stopped with the following message: ${workflow.errorMessage}"
-}
-```
-
-:::{note}
-Both the `onError` and `onComplete` handlers are invoked when an error condition is encountered. The first is called as soon as the error is raised, while the second is called just before the pipeline execution is about to terminate. When using the `finish` {ref}`process-error-strategy`, there may be a significant gap between the two, depending on the time required to complete any pending job.
-:::
-
-## Decoupling metadata
-
-The workflow event handlers can be defined also in the `nextflow.config` file. This is useful to decouple the handling of pipeline events from the main script logic.
-
-When the event handlers are included in a configuration file the only difference is that the `onComplete` and the `onError` closures have to be defined by using the assignment operator as shown below:
-
-```groovy
-workflow.onComplete = {
-    // any workflow property can be used here
-    println "Pipeline complete"
-    println "Command line: $workflow.commandLine"
-}
-
-workflow.onError = {
-    println "Error: something when wrong"
-}
-```
-
-:::{note}
-It is possible to define workflow event handlers both in the pipeline script **and** in the configuration file.
-:::
diff --git a/docs/metrics.md b/docs/metrics.md
index 0681328ab6..eac8ae0e3d 100644
--- a/docs/metrics.md
+++ b/docs/metrics.md
@@ -1,8 +1,8 @@
 (metrics-page)=
 
-# Metrics
+# Understanding task resource metrics
 
-This section details how the resource usage metrics from the {ref}`Execution report <execution-report>` are computed.
+This tutorial explains how the resource usage metrics from the {ref}`Execution report <execution-report>` are computed.
 
 ## CPU Usage
 
@@ -15,12 +15,13 @@ Let's illustrate how this plot behaves with several examples.
 
 In the first example, let's consider the simple use case in which a process performs one task of pure computation using one CPU. Then, you expect the `Raw Usage` tab to report 100%. If the task is distributed over, 2, 3, 4, `etc.` CPUs, then the `Raw Usage` will be 200%, 300%, 400%, `etc.` respectively. The `% Allocated` tab just rescales the raw value usage with respect to the number of CPUs set with the `cpus` directive (if not set with the directive, the number of CPUs is set to 1, thus showing the same values as in the `Raw Usage` tab). Using the program [stress](https://people.seas.harvard.edu/~apw/stress/) as follows would report 100% in the `Raw Usage` tab and 50% in the `% Allocated` tab since the process asked twice the number of CPUs needed by the process:
 
-```groovy
+```nextflow
 #!/usr/bin/env nextflow
 
 process CpuUsageEx1 {
   cpus 2
 
+  script:
   """
   stress -c 1 -t 10 # compute square-root of random numbers during 10s using 1 CPU
   """
@@ -29,12 +30,13 @@ process CpuUsageEx1 {
 
 In the second example, some time will be spent performing pure computation and some time just waiting. Using the program [stress](https://people.seas.harvard.edu/~apw/stress/) and `sleep` as follows would report 75% in the `Raw Usage` tab:
 
-```groovy
+```nextflow
 #!/usr/bin/env nextflow
 
 process CpuUsageEx2 {
   cpus 1
 
+  script:
   """
   stress -c 1 -t 10 # compute square-root of random numbers during 10s using 1 CPU
   stress -c 1 -t 5 # compute square-root of random numbers during 5s using 1 CPU
@@ -51,12 +53,13 @@ $$
 
 The third example is similar to the second one except that the pure computation stage is performed in a single step forked on 2 CPUs:
 
-```groovy
+```nextflow
 #!/usr/bin/env nextflow
 
 process CpuUsageEx3 {
   cpus 2
 
+  script:
   """
   stress -c 2 -t 10 # compute square-root of random numbers during 10s using 2 CPUs
   sleep 10 # use no CPU during 10s
@@ -226,12 +229,13 @@ int main(int argc, char **argv) {
 
 The first and second programs are executed in `foo` and `bar` processes respectively as follows:
 
-```groovy
+```nextflow
 #!/usr/bin/env nextflow
 
 process foo {
     memory '1.5 GB'
 
+    script:
     """
     memory_vmem_1GiB_ram_0Gib
     """
@@ -240,6 +244,7 @@ process foo {
 process bar {
     memory '1.5 GB'
 
+    script:
     """
     memory_vmem_1GiB_ram_1Gib
     """
@@ -276,7 +281,7 @@ The plot has two tabs the job duration (a.k.a. elapsed real time, real time or w
 
 The plot has two tabs showing how many data were read and/or written each process. For example, the following processes read and write 1GB and 256MB of data respectively:
 
-```groovy
+```nextflow
 #!/usr/bin/env nextflow
 
 process io_read_write_1G {
diff --git a/docs/module.md b/docs/module.md
index abf07a350b..c9dae998ff 100644
--- a/docs/module.md
+++ b/docs/module.md
@@ -2,7 +2,7 @@
 
 # Modules
 
-In Nextflow, a **module** is a script that may contain functions, processes, and workflows (collectively referred to as *components*). A module can be included in other modules or pipeline scripts and even shared across workflows.
+Nextflow scripts can include **definitions** (workflows, processes, and functions) from other scripts. When a script is included in this way, it is referred to as a **module**. Modules can be included by other modules or pipeline scripts and can even be shared across workflows.
 
 :::{note}
 Modules were introduced in DSL2. If you are still using DSL1, see the {ref}`dsl1-page` page to learn how to migrate your Nextflow pipelines to DSL2.
@@ -10,11 +10,11 @@ Modules were introduced in DSL2. If you are still using DSL1, see the {ref}`dsl1
 
 ## Module inclusion
 
-A component defined in a module script can be imported into another Nextflow script using the `include` keyword.
+You can include any definition from a module into a Nextflow script using the `include` keyword.
 
 For example:
 
-```groovy
+```nextflow
 include { foo } from './some/module'
 
 workflow {
@@ -23,7 +23,7 @@ workflow {
 }
 ```
 
-The above snippet imports a process named `foo`, defined in the module script, into the main execution context. This way, `foo` can be invoked in the `workflow` scope.
+The above snippet imports a process named `foo`, defined in the module, into the main execution context. This way, `foo` can be invoked in the `workflow` scope.
 
 Nextflow implicitly looks for the script file `./some/module.nf`, resolving the path against the *including* script location.
 
@@ -49,7 +49,7 @@ some
 
 When defined as a directory, the module must be included by specifying the module directory path:
 
-```groovy
+```nextflow
 include { foo } from './some/module'
 ```
 
@@ -57,9 +57,9 @@ Module directories allow the use of module scoped binaries scripts. See [Module
 
 ## Multiple inclusions
 
-A Nextflow script can include any number of modules, and an `include` statement can import any number of components from a module. Multiple components can be included from the same module by using the syntax shown below:
+A Nextflow script can include any number of modules, and an `include` statement can import any number of definitions from a module. Multiple definitions can be included from the same module by using the syntax shown below:
 
-```groovy
+```nextflow
 include { foo; bar } from './some/module'
 
 workflow {
@@ -73,9 +73,9 @@ workflow {
 
 ## Module aliases
 
-When including a module component, it's possible to specify an *alias* with the `as` keyword. Aliasing allows you to avoid module name clashes, by assigning them different names in the including context. For example:
+When including definition from a module, it's possible to specify an *alias* with the `as` keyword. Aliasing allows you to avoid module name clashes, by assigning them different names in the including context. For example:
 
-```groovy
+```nextflow
 include { foo } from './some/module'
 include { foo as bar } from './other/module'
 
@@ -85,9 +85,9 @@ workflow {
 }
 ```
 
-You can even include the same component multiple times under different names:
+You can also include the same definition multiple times under different names:
 
-```groovy
+```nextflow
 include { foo; foo as bar } from './some/module'
 
 workflow {
@@ -96,15 +96,17 @@ workflow {
 }
 ```
 
+(module-params)=
+
 ## Module parameters
 
 :::{deprecated} 24.07.0-edge
-As a best practice, parameters should be used in the entry workflow and passed to functions / processes / workflows as explicit inputs.
+As a best practice, parameters should be used in the entry workflow and passed to workflows, processes, and functions as explicit inputs.
 :::
 
-A module script can define parameters using the same syntax as a Nextflow workflow script:
+A module can define parameters using the same syntax as a Nextflow workflow script:
 
-```groovy
+```nextflow
 params.foo = 'Hello'
 params.bar = 'world!'
 
@@ -115,7 +117,7 @@ def sayHello() {
 
 When including a module, the module will first use parameters from the including context. For example:
 
-```groovy
+```nextflow
 params.foo = 'Hola'
 params.bar = 'Mundo'
 
@@ -142,7 +144,7 @@ It is best to define all pipeline parameters *before* any `include` statements.
 
 The `addParams` option can be used to pass parameters to the module without adding them to the including scope.
 
-```groovy
+```nextflow
 params.foo = 'Hola'
 params.bar = 'Mundo'
 
@@ -161,7 +163,7 @@ Ciao Mundo
 
 Alternatively, the `params` option can be used to pass parameters to module without adding them to the including scope, *and* without inheriting any parameters from the including scope.
 
-```groovy
+```nextflow
 params.foo = 'Hola'
 params.bar = 'Mundo'
 
@@ -182,9 +184,9 @@ Ciao world!
 
 ## Module templates
 
-The module script can be defined in an external {ref}`template <process-template>` file. The template file can be placed in the `templates` directory where the module script is located.
+Process script {ref}`templates <process-template>` can be included alongside a module in the `templates` directory.
 
-For example, suppose we have a project L with a module script that defines two processes, P1 and P2, both of which use templates. The template files can be made available in the local `templates` directory:
+For example, suppose we have a project L with a module that defines two processes, P1 and P2, both of which use templates. The template files can be made available in the local `templates` directory:
 
 ```
 Project L
@@ -208,15 +210,15 @@ Pipeline B
 └── main.nf
 ```
 
-With the possibility to keep the template files inside the project L, A and B can use the modules defined in L without any changes. A future project C would do the same, just cloning L (if not available on the system) and including its module script.
+With the possibility to keep the template files inside the project L, A and B can use the modules defined in L without any changes. A future project C would do the same, just cloning L (if not available on the system) and including its module.
 
 Beside promoting the sharing of modules across pipelines, there are several advantages to keeping the module template under the script path:
 
-1. module components are *self-contained*,
-2. module components can be tested independently from the pipeline(s) that import them,
-3. it is possible to create libraries of module components.
+1. Modules are self-contained
+2. Modules can be tested independently from the pipeline(s) that import them
+3. Modules can be made into libraries
 
-Ultimately, having multiple template locations allows a more structured organization within the same project. If a project has several module components, and all of them use templates, the project could group module scripts and their templates as needed. For example:
+Having multiple template locations enables a structured project organization. If a project has several modules, and they all use templates, the project could group module scripts and their templates as needed. For example:
 
 ```
 baseDir
@@ -251,9 +253,9 @@ baseDir
 
 Modules can define binary scripts that are locally scoped to the processes defined by the tasks.
 
-To enable this feature, enable the following flag in your pipeline configuration file:
+To enable this feature, set the following flag in your pipeline script or configuration file:
 
-```groovy
+```nextflow
 nextflow.enable.moduleBinaries = true
 ```
 
diff --git a/docs/mail.md b/docs/notifications.md
similarity index 79%
rename from docs/mail.md
rename to docs/notifications.md
index a554856451..9f58f56fd4 100644
--- a/docs/mail.md
+++ b/docs/notifications.md
@@ -1,8 +1,45 @@
 (mail-page)=
 
-# Mail & Notifications
+# Notifications
 
-## Mail message
+This page documents how to handle workflow events and send notifications.
+
+(workflow-handlers)=
+
+## Workflow handlers
+
+(metadata-completion-handler)=
+
+### Completion handler
+
+Due to the asynchronous nature of Nextflow the termination of a script does not correspond to the termination of the running workflow. Thus some information, only available on execution completion, needs to be accessed by using an asynchronous handler.
+
+The `onComplete` event handler is invoked by the framework when the workflow execution is completed. It allows one to access the workflow termination status and other useful information. For example:
+
+```nextflow
+workflow.onComplete {
+    println "Pipeline completed at: $workflow.complete"
+    println "Execution status: ${ workflow.success ? 'OK' : 'failed' }"
+}
+```
+
+(metadata-error-handler)=
+
+### Error handler
+
+The `onError` event handler is invoked by Nextflow when a runtime or process error caused the pipeline execution to stop. For example:
+
+```nextflow
+workflow.onError {
+    println "Error: Pipeline execution stopped with the following message: ${workflow.errorMessage}"
+}
+```
+
+:::{note}
+Both the `onError` and `onComplete` handlers are invoked when an error condition is encountered. The first is called as soon as the error is raised, while the second is called just before the pipeline execution is about to terminate. When using the `finish` {ref}`process-error-strategy`, there may be a significant gap between the two, depending on the time required to complete any pending job.
+:::
+
+## Mail
 
 The built-in function `sendMail` allows you to send a mail message from a workflow script.
 
@@ -12,7 +49,7 @@ The built-in function `sendMail` allows you to send a mail message from a workfl
 
 The mail attributes are specified as named parameters or an equivalent map. For example:
 
-```groovy
+```nextflow
 sendMail(
     to: 'you@gmail.com',
     subject: 'Catch up',
@@ -23,7 +60,7 @@ sendMail(
 
 which is equivalent to:
 
-```groovy
+```nextflow
 mail = [
     to: 'you@gmail.com',
     subject: 'Catch up',
@@ -76,7 +113,7 @@ The following parameters can be specified:
 
 Another version of `sendMail` allows a more idiomatic syntax:
 
-```groovy
+```nextflow
 sendMail {
     to 'you@gmail.com'
     from 'me@gmail.com'
@@ -124,7 +161,7 @@ Moreover for each attachment it's possible to specify any of the following optio
 
 For example:
 
-```groovy
+```nextflow
 sendMail {
     to 'you@dot.com'
     attach '/some/file.txt', fileName: 'manuscript.txt'
@@ -178,7 +215,7 @@ ses:SendRawEmail
 
 You can use the `sendMail` function with a {ref}`workflow completion handler <metadata-completion-handler>` to notify the completion of a workflow completion. For example:
 
-```groovy
+```nextflow
 workflow.onComplete {
 
     def msg = """\
diff --git a/docs/overview.md b/docs/overview.md
index f848facde4..44b1a3cb8a 100644
--- a/docs/overview.md
+++ b/docs/overview.md
@@ -20,7 +20,7 @@ Any process can define one or more channels as *input* and *output*. The interac
 
 A Nextflow script looks like this:
 
-```groovy
+```nextflow
 // Script parameters
 params.query = "/some/data/sample.fa"
 params.db = "/some/path/pdb"
@@ -33,6 +33,7 @@ process blastSearch {
   output:
   path "top_hits.txt"
 
+  script:
   """
   blastp -db $db -query $query -outfmt 6 > blast_result
   cat blast_result | head -n 10 | cut -f 2 > top_hits.txt
@@ -47,6 +48,7 @@ process extractTopHits {
   output:
   path "sequences.txt"
 
+  script:
   """
   blastdbcmd -db $db -entry_batch $top_hits > sequences.txt
   """
@@ -95,11 +97,9 @@ Read the {ref}`executor-page` to learn more about the Nextflow executors.
 
 ## Scripting language
 
-Nextflow is designed to have a minimal learning curve, without having to pick up a new programming language. In most cases, users can utilise their current skills to develop Nextflow workflows. However, it also provides a powerful scripting DSL.
-
-Nextflow scripting is an extension of the [Groovy programming language](<http://en.wikipedia.org/wiki/Groovy_(programming_language)>), which in turn is a super-set of the Java programming language. Groovy can be considered as Python for Java in that it simplifies the writing of code and is more approachable.
+Nextflow is a workflow language based on [Java](https://en.wikipedia.org/wiki/Java_(programming_language)) and [Groovy](https://groovy-lang.org/). It is designed to simplify writing scalable and reproducible pipelines. In most cases, users can leverage their existing programming skills to develop Nextflow pipelines without the steep learning curve that usually comes with a new programming language.
 
-Read the {ref}`script-page` section to learn about the Nextflow scripting language.
+See {ref}`script-page` for more information about the Nextflow scripting language.
 
 ## Configuration options
 
diff --git a/docs/plugins.md b/docs/plugins.md
index b1fca44024..3f0f73773e 100644
--- a/docs/plugins.md
+++ b/docs/plugins.md
@@ -18,7 +18,6 @@ The following functionalities are provided via plugin components, and they make
 - `nf-tower`: Support for [Seqera Platform](https://seqera.io) (formerly Tower Cloud).
 - `nf-wave`: Support for [Wave containers](https://seqera.io/wave/) service.
 
-
 ## Using plugins
 
 The core plugins do not require any configuration. They are automatically installed when the corresponding feature is requested by a Nextflow pipeline. You can still specify them as described below, e.g. if you want to pin the version of a plugin, however if you try to use a plugin version that isn't compatible with your Nextflow version, Nextflow will fail.
@@ -43,347 +42,11 @@ The plugin version is optional. If it is not specified, Nextflow will download t
 
 The core plugins are documented in this documentation. For all other plugins, please refer to the plugin's code repository for documentation and support.
 
-## Writing plugins
-
-To get started with your own plugin, refer to the [nf-hello](https://github.com/nextflow-io/nf-hello) repository, which provides a minimal plugin implementation with several examples of different extension points, as well as instructions for building, testing, and publishing.
-
-Nextflow's plugin system exposes a variety of extension points for plugins. The following sections describe how to use these extension points when writing a plugin, as well as how they are used in a pipeline.
-
-:::{note}
-If you would like to implement something in a plugin that isn't covered by any of the following sections, feel free to create an issue on GitHub and describe your use case. In general, any class in the Nextflow codebase that implements `ExtensionPoint` can be extended by a plugin, and existing plugins are a great source of examples when writing new plugins.
-:::
-
-:::{note}
-Plugin extension points must be added to `extensions.idx` in the plugin repository to make them discoverable. See the `nf-hello` plugin for an example.
-:::
-
-### Commands
-
-Plugins can define custom CLI commands that can be executed with the `nextflow plugin` command.
-
-To implement a plugin-specific command, implement the `PluginExecAware` interface in your plugin entrypoint (the class that extends `BasePlugin`). Alternatively, you can implement the `PluginAbstractExec` trait, which provides an abstract implementation with some boilerplate code. This trait requires you to implement two methods, `getCommands()` and `exec()`:
-
-```groovy
-import nextflow.cli.PluginAbstractExec
-import nextflow.plugin.BasePlugin
-
-class MyPlugin extends BasePlugin implements PluginAbstractExec {
-    @Override
-    List<String> getCommands() {
-        [ 'hello' ]
-    }
-
-    @Override
-    int exec(String cmd, List<String> args) {
-        if( cmd == 'hello' ) {
-            println "Hello! You gave me these arguments: ${args.join(' ')}"
-            return 0
-        }
-        else {
-            System.err.println "Invalid command: ${cmd}"
-            return 1
-        }
-    }
-}
-```
-
-You can then execute this command using the `nextflow plugin` command:
-
-```bash
-nextflow plugin my-plugin:hello --foo --bar
-```
-
-See the {ref}`cli-plugin` CLI command for usage information.
-
-### Configuration
-
-Plugins can access the resolved Nextflow configuration through the session object using `session.config.navigate()`. Several extension points provide the session object for this reason. This method allows you to query any configuration option in a safe manner -- if the option isn't defined, it will return `null`. A common practice is to define any configuration for your plugin in a custom config scope.
-
-Here is an example of querying a config option in a trace observer hook:
-
-```groovy
-import nextflow.Session
-import nextflow.trace.TraceObserver
-
-class MyObserver implements TraceObserver {
-
-    @Override
-    void onFlowCreate(Session session) {
-        final message = session.config.navigate('myplugin.create.message')
-        println message
-    }
-}
-```
-
-You can then set this option in your config file:
-
-```groovy
-// dot syntax
-myplugin.create.message = "I'm alive!"
-
-// closure syntax
-myplugin {
-    create {
-        message = "I'm alive!"
-    }
-}
-```
-
-### Executors
-
-Plugins can define custom executors that can then be used with the `executor` process directive.
-
-To implement an executor, create a class in your plugin that extends the [`Executor`](https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/executor/Executor.groovy) class and implements the `ExtensionPoint` interface. Add the `@ServiceName` annotation to your class with the name of your executor:
-
-```groovy
-import nextflow.executor.Executor
-import nextflow.util.ServiceName
-import org.pf4j.ExtensionPoint
-
-@ServiceName('my-executor')
-class MyExecutor extends Executor implements ExtensionPoint {
-
-    // ...
-
-}
-```
-
-You can then use this executor in your pipeline:
-
-```groovy
-process foo {
-    executor 'my-executor'
-}
-```
-
-:::{tip}
-Refer to the source code of Nextflow's built-in executors to see how to implement the various components of an executor. You might be able to implement most of your executor by simply reusing existing code.
-:::
-
-### Functions
-
-:::{versionadded} 22.09.0-edge
-:::
-
-Plugins can define custom Groovy functions, which can then be included into Nextflow pipelines.
-
-To implement a custom function, create a class in your plugin that extends the `PluginExtensionPoint` class, and implement your function with the `Function` annotation:
-
-```groovy
-import nextflow.Session
-import nextflow.plugin.extension.Function
-import nextflow.plugin.extension.PluginExtensionPoint
-
-class MyExtension extends PluginExtensionPoint {
-
-    @Override
-    void init(Session session) {}
-
-    @Function
-    String reverseString(String origin) {
-        origin.reverse()
-    }
-
-}
-```
-
-You can then use this function in your pipeline:
-
-```groovy
-include { reverseString } from 'plugin/my-plugin'
-
-channel.of( reverseString('hi') )
-```
-
-You can also use an alias:
-
-```groovy
-include { reverseString as anotherReverseMethod } from 'plugin/my-plugin'
-```
-
-### Operators
-
-:::{versionadded} 22.04.0
-:::
-
-Plugins can define custom channel factories and operators, which can then be included into Nextflow pipelines.
-
-To implement a custom factory or operator, create a class in your plugin that extends the `PluginExtensionPoint` class, and implement your function with the `Factory` or `Operator` annotation:
-
-```groovy
-import groovyx.gpars.dataflow.DataflowReadChannel
-import groovyx.gpars.dataflow.DataflowWriteChannel
-import nextflow.Session
-import nextflow.plugin.extension.Factory
-import nextflow.plugin.extension.Operator
-import nextflow.plugin.extension.PluginExtensionPoint
-
-class MyExtension extends PluginExtensionPoint {
-
-    @Override
-    void init(Session session) {}
-
-    @Factory
-    DataflowWriteChannel fromQuery(Map opts, String query) {
-        // ...
-    }
-
-    @Operator
-    DataflowWriteChannel sqlInsert(DataflowReadChannel source, Map opts) {
-        // ...
-    }
-
-}
-```
-
-You can then use them in your pipeline:
-
-```groovy
-include { sqlInsert; fromQuery as fromTable } from 'plugin/nf-sqldb'
-
-def sql = 'select * from FOO'
-channel
-    .fromTable(sql, db: 'test', emitColumns: true)
-    .sqlInsert(into: 'BAR', columns: 'id', db: 'test')
-```
-
-The above snippet is based on the [nf-sqldb](https://github.com/nextflow-io/nf-sqldb) plugin. The `fromQuery` factory 
-is included under the alias `fromTable`.
-
-### Process directives
-
-Plugins that implement a [custom executor](#executors) will likely need to access {ref}`process directives <process-directives>` that affect the task execution. When an executor receives a task, the process directives can be accessed through that task's configuration. As a best practice, custom executors should try to support all process directives that have executor-specific behavior and are relevant to your executor.
-
-Nextflow does not provide the ability to define custom process directives in a plugin. Instead, you can use the {ref}`process-ext` directive to provide custom process settings to your executor. Try to use specific names that are not likely to conflict with other plugins or existing pipelines.
-
-Here is an example of a custom executor that uses existing process directives as well as a custom setting through the `ext` directive:
-
-```groovy
-class MyExecutor extends Executor {
-
-    @Override
-    TaskHandler createTaskHandler(TaskRun task) {
-        final cpus = task.config.cpus
-        final memory = task.config.memory
-        final myOption = task.config.ext.myOption
-
-        println "This task is configured with cpus=${cpus}, memory=${memory}, myOption=${myOption}"
-
-        // ...
-    }
-
-    // ...
-
-}
-```
-
-### Trace observers
-
-A *trace observer* in Nextflow is an entity that can listen and react to workflow events, such as when a workflow starts, a task completes, a file is published, etc. Several components in Nextflow, such as the execution report and DAG visualization, are implemented as trace observers.
-
-Plugins can define custom trace observers that react to workflow events with custom behavior. To implement a trace observer, create a class that implements the `TraceObserver` trait and another class that implements the `TraceObserverFactory` interface. Implement any of the hooks defined in `TraceObserver`, and implement the `create()` method in your observer factory:
-
-```groovy
-// MyObserverFactory.groovy
-import nextflow.Session
-import nextflow.trace.TraceObserver
-import nextflow.trace.TraceObserverFactory
-
-class MyObserverFactory implements TraceObserverFactory {
-
-    @Override
-    Collection<TraceObserver> create(Session session) {
-        final enabled = session.config.navigate('myplugin.enabled')
-        return enabled ? [ new MyObserver() ] : []
-    }
-}
-
-// MyObserver.groovy
-import java.nio.file.Path
-
-import nextflow.processor.TaskHandler
-import nextflow.trace.TraceObserver
-import nextflow.trace.TraceRecord
-
-class MyObserver implements TraceObserver {
-    
-    @Override
-    void onFlowBegin() {
-        println "Okay, let's begin!"
-    }
-
-    @Override
-    void onProcessComplete(TaskHandler handler, TraceRecord trace) {
-        println "I completed a task! It's name is '${handler.task.name}'"
-    }
-
-    @Override
-    void onProcessCached(TaskHandler handler, TraceRecord trace) {
-        println "I found a task in the cache! It's name is '${handler.task.name}'"
-    }
-
-    @Override
-    void onFilePublish(Path destination, Path source) {
-        println "I published a file! It's located at ${path.toUriString()}"
-    }
-    
-    @Override
-    void onFlowError(TaskHandler handler, TraceRecord trace) {
-        println "Uh oh, something went wrong..."
-    }
-
-    @Override
-    void onFlowComplete() {
-        println 'All done!'
-    }
-}
-```
-
-You can then use your trace observer by simply enabling the plugin in your pipeline. In the above example, the observer must also be enabled with a config option:
-
-```groovy
-myplugin.enabled = true
-```
-
-Refer to the `TraceObserver` [source code](https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/trace/TraceObserver.groovy) for descriptions of the available workflow events.
-
-## Plugin registry
-
-Nextflow resolves plugins through a plugin registry, which stores metadata for each plugin version, including the publishing date, checksum, and download URL for the plugin binary. The default registry is located on GitHub at [nextflow-io/plugins](https://github.com/nextflow-io/plugins/).
-
-To publish a plugin release to the main registry, simply create a pull request with the requested plugin metadata.
-
-(testing-plugins)=
-
-### Testing plugins
-
-:::{versionadded} 23.04.0
-:::
-
-You can also use a different plugin registry with the `NXF_PLUGINS_TEST_REPOSITORY` environment variable. This setting is useful for testing a plugin release before publishing it to the main registry. It can refer to the JSON file for a custom registry or a plugin release.
-
-For example:
-
-```bash
-# custom plugin repository at https://github.com/my-org/plugins
-export NXF_PLUGINS_TEST_REPOSITORY="https://raw.githubusercontent.com/my-org/plugins/main/plugins.json"
-
-# custom plugin release
-export NXF_PLUGINS_TEST_REPOSITORY="https://github.com/nextflow-io/nf-hello/releases/download/0.3.0/nf-hello-0.3.0-meta.json"
-
-nextflow run <pipeline> -plugins nf-hello
-```
-
-:::{tip}
-This variable can be either the URI of a plugins repository JSON file or the URI of a specific plugin JSON meta file.
-In the latter case it should match the pattern `https://host.name/some/path/<plugin id>-X.Y.Z-meta.json`.
-:::
-
 ## Offline usage
 
 To use Nextflow plugins in an offline environment:
 
-1. {ref}`Download Nextflow <install-nextflow>` and install it on a system with an internet connection. Do not use the "all" package, as this does not allow the use of custom plugins.
+1. {ref}`Install Nextflow <install-nextflow>` on a system with an internet connection. Do not use the "all" package, as this does not allow the use of custom plugins.
 
 2. Download any additional plugins by running `nextflow plugin install <pluginId,..>`. Alternatively, simply run your pipeline once and Nextflow will download all of the plugins that it needs.
 
diff --git a/docs/process.md b/docs/process.md
index da05dfcf32..871ecea093 100644
--- a/docs/process.md
+++ b/docs/process.md
@@ -2,39 +2,23 @@
 
 # Processes
 
-In Nextflow, a **process** is the basic processing primitive to execute a user script.
+In Nextflow, a **process** is a specialized function for executing scripts in a scalable and portable manner.
 
-The process definition starts with the keyword `process`, followed by process name and finally the process body delimited by curly braces. The process body must contain a string which represents the command or, more generally, a script that is executed by it. A basic process looks like the following example:
+Here is an example process definition:
 
-```groovy
+```nextflow
 process sayHello {
+    output:
+    path 'hello.txt'
+
+    script:
     """
-    echo 'Hello world!' > file
+    echo 'Hello world!' > hello.txt
     """
 }
 ```
 
-A process may contain any of the following definition blocks: directives, inputs, outputs, when clause, and the process script. The syntax is defined as follows:
-
-```
-process < name > {
-
-  [ directives ]
-
-  input:
-    < process inputs >
-
-  output:
-    < process outputs >
-
-  when:
-    < condition >
-
-  [script|shell|exec]:
-    < user script to be executed >
-
-}
-```
+See {ref}`syntax-process` for a full description of the process syntax.
 
 (process-script)=
 
@@ -48,7 +32,7 @@ The script string is executed as a [Bash](<http://en.wikipedia.org/wiki/Bash_(Un
 
 The script block can be a simple string or a multi-line string. The latter approach makes it easier to write scripts with multiple commands spanning multiple lines. For example:
 
-```groovy
+```nextflow
 process doMoreThings {
   """
   blastp -db $db -query query.fa -outfmt 6 > blast_result
@@ -72,7 +56,7 @@ When you need to access a system environment variable in your script, you have t
 
 If you don't need to access any Nextflow variables, you can define your script block with single-quotes:
 
-```groovy
+```nextflow
 process printPath {
   '''
   echo The path is: $PATH
@@ -82,7 +66,7 @@ process printPath {
 
 Otherwise, you can define your script with double-quotes and escape the system environment variables by prefixing them with a back-slash `\` character, as shown in the following example:
 
-```groovy
+```nextflow
 process doOtherThings {
   """
   blastp -db \$DB -query query.fa -outfmt 6 > blast_result
@@ -108,7 +92,7 @@ A pipeline may be composed of processes that execute very different tasks. With
 
 To use a language other than Bash, simply start your process script with the corresponding [shebang](<http://en.wikipedia.org/wiki/Shebang_(Unix)>). For example:
 
-```groovy
+```nextflow
 process perlTask {
     """
     #!/usr/bin/perl
@@ -139,11 +123,11 @@ Since the actual location of the interpreter binary file can differ across platf
 
 ### Conditional scripts
 
-So far, our `script` block has always been a simple string expression, but in reality, the `script` block is just Groovy code that returns a string. This means that you can write arbitrary Groovy code to determine the script to execute, as long as the final statement is a string (remember that the `return` keyword is optional in Groovy).
+The `script` block is like a function that returns a string. This means that you can write arbitrary code to determine the script, as long as the final statement is a string.
 
-For example, you can use flow control statements (`if`, `switch`, etc) to execute a different script based on the process inputs. The only difference here is that you must explicitly declare the `script` guard, whereas before it was not required. Here is an example:
+If-else statements based on task inputs can be used to produce a different script. For example:
 
-```groovy
+```nextflow
 mode = 'tcoffee'
 
 process align {
@@ -171,17 +155,17 @@ process align {
 }
 ```
 
-In the above example, the process will execute one of the script fragments depending on the value of the `mode` parameter. By default it will execute the `tcoffee` command, but changing the `mode` variable will cause a different branch to be executed.
+In the above example, the process will execute one of several scripts depending on the value of the `mode` parameter. By default it will execute the `tcoffee` command.
 
 (process-template)=
 
 ### Template
 
-Process scripts can be externalised to **template** files, which can be reused across different processes and tested independently from the overall pipeline execution.
+Process scripts can be externalized to **template** files, which allows them to be reused across different processes and tested independently from the pipeline execution.
 
-A template is simply a shell script file that Nextflow is able to execute by using the `template` function as shown below:
+A template can be used in place of an embedded script using the `template` function in the script section:
 
-```groovy
+```nextflow
 process templateExample {
     input:
     val STR
@@ -195,9 +179,9 @@ workflow {
 }
 ```
 
-By default, Nextflow looks for the `my_script.sh` template file in the `templates` directory located alongside the Nextflow script and/or the module script in which the process is defined. Any other location can be specified by using an absolute template path.
+By default, Nextflow looks for the template script in the `templates` directory located alongside the Nextflow script in which the process is defined. An absolute path can be used to specify a different location. However, this practice is discouraged because it hinders pipeline portability.
 
-The template script may contain any code that can be executed by the underlying environment. For example:
+An example template script is provided below:
 
 ```bash
 #!/bin/bash
@@ -206,23 +190,37 @@ echo $STR
 echo "process completed"
 ```
 
-:::{tip}
-The dollar character (`$`) is interpreted as a Nextflow variable when the script is run as a Nextflow template, whereas it is evaluated as a Bash variable when run as a Bash script. This can be very useful for testing your script independently from Nextflow execution. You only need to provide a Bash environment variable for each of the Nextflow variables that are referenced in your script. For example, it would be possible to execute the above script with the following command in the terminal: `STR='foo' bash templates/my_script.sh`
-:::
+Variables prefixed with the dollar character (`$`) are interpreted as Nextflow variables when the template script is executed by Nextflow and Bash variables when executed directly. For example, the above script can be executed from the command line by providing each input as an environment variable:
+
+```bash
+STR='foo' bash templates/my_script.sh
+```
+
+The following caveats should be considered:
+
+- Template scripts are recommended only for Bash scripts. Languages that do not prefix variables with `$` (e.g. Python and R) can't be executed directly as a template script.
+
+- Variables escaped with `\$` will be interpreted as Bash variables when executed by Nextflow, but will not be interpreted as variables when executed from the command line. This practice should be avoided to ensure that the template script behaves consistently.
+
+- Template variables are evaluated even if they are commented out in the template script. If a template variable is missing, it will cause the pipeline to fail regardless of where it occurs in the template.
 
 :::{tip}
-As a best practice, the template script should not contain any `\$` escaped variables, because these variables will not be evaluated properly when the script is executed directly.
+Template scripts are generally discouraged due to the caveats described above. The best practice for using a custom script is to embed it in the process definition at first and move it to a separate file with its own command line interface once the code matures.
 :::
 
 (process-shell)=
 
 ### Shell
 
+:::{deprecated} 24.11.0-edge
+Use the `script` block instead. Consider using the {ref}`VS Code extension <vscode-page>`, which provides syntax highlighting and error checking to distinguish Nextflow variables from Bash variables in the process script.
+:::
+
 The `shell` block is a string expression that defines the script that is executed by the process. It is an alternative to the {ref}`process-script` definition with one important difference: it uses the exclamation mark `!` character, instead of the usual dollar `$` character, to denote Nextflow variables.
 
 This way, it is possible to use both Nextflow and Bash variables in the same script without having to escape the latter, which makes process scripts easier to read and maintain. For example:
 
-```groovy
+```nextflow
 process myTask {
     input:
     val str
@@ -243,18 +241,18 @@ In the above example, `$USER` is treated as a Bash variable, while `!{str}` is t
 :::{note}
 - Shell script definitions require the use of single-quote `'` delimited strings. When using double-quote `"` delimited strings, dollar variables are interpreted as Nextflow variables as usual. See {ref}`string-interpolation`.
 - Variables prefixed with `!` must always be enclosed in curly brackets, i.e. `!{str}` is a valid variable whereas `!str` is ignored.
-- Shell scripts support the use of the {ref}`process-template` mechanism. The same rules are applied to the variables defined in the script template.
+- Shell scripts support the use of the {ref}`process-template` mechanism. The same rules are applied to the variables defined in the template script.
 :::
 
 (process-native)=
 
 ### Native execution
 
-Nextflow processes can also execute native Groovy code as the task itself, using the `exec` block. Whereas the `script` block defines a script to be executed, the `exec` block defines Groovy code to be executed directly.
+The `exec` block executes the given code without launching a job.
 
 For example:
 
-```groovy
+```nextflow
 process simpleSum {
     input:
     val x
@@ -276,6 +274,8 @@ Hello Mr. a
 Hello Mr. c
 ```
 
+A native process is very similar to a {ref}`function <syntax-function>`. However, it provides additional capabilities such as parallelism, caching, and progress logging.
+
 (process-stub)=
 
 ## Stub
@@ -285,7 +285,7 @@ Hello Mr. c
 
 You can define a command *stub*, which replaces the actual process command when the `-stub-run` or `-stub` command-line option is enabled:
 
-```groovy
+```nextflow
 process INDEX {
   input:
     path transcriptome
@@ -332,23 +332,27 @@ When a process is invoked in a workflow block, it must be provided a channel for
 The following input qualifiers are available:
 
 - `val`: Access the input value by name in the process script.
-- `file`: (DEPRECATED) Handle the input value as a file, staging it properly in the execution context.
 - `path`: Handle the input value as a path, staging the file properly in the execution context.
 - `env`: Use the input value to set an environment variable in the process script.
 - `stdin`: Forward the input value to the process `stdin` special file.
 - `tuple`: Handle a group of input values having any of the above qualifiers.
 - `each`: Execute the process for each element in the input collection.
 
-### Input type `val`
+See {ref}`process reference <process-reference-inputs>` for the full list of input methods and options.
+
+### Input variables (`val`)
 
 The `val` qualifier accepts any data type. It can be accessed in the process script by using the specified input name, as shown in the following example:
 
-```groovy
+```nextflow
 process basicExample {
   input:
   val x
 
-  "echo process job $x"
+  script:
+  """
+  echo process job $x
+  """
 }
 
 workflow {
@@ -372,12 +376,15 @@ While channels do emit items in the order that they are received, *processes* do
 :::{note}
 When the process declares exactly one input, the pipe `|` operator can be used to provide inputs to the process, instead of passing it as a parameter. Both methods have identical semantics:
 
-```groovy
+```nextflow
 process basicExample {
   input:
   val x
 
-  "echo process job $x"
+  script:
+  """
+  echo process job $x
+  """
 }
 
 workflow {
@@ -386,26 +393,21 @@ workflow {
 ```
 :::
 
-### Input type `file`
-
-:::{note}
-The `file` qualifier was the standard way to handle input files prior to Nextflow 19.10.0. In later versions of Nextflow, the `path` qualifier should be preferred over `file`.
-:::
-
-The `file` qualifier is identical to `path`, with one important difference. When a `file` input receives a value that is not a file, it automatically converts the value to a string and saves it to a temporary file. This behavior is useful in some cases, but tends to be confusing in general. The `path` qualifier instead interprets string values as the path location of the input file and automatically converts to a file object.
-
 (process-input-path)=
 
-### Input type `path`
+### Input files (`path`)
 
 The `path` qualifier allows you to provide input files to the process execution context. Nextflow will stage the files into the process execution directory, and they can be accessed in the script by using the specified input name. For example:
 
-```groovy
+```nextflow
 process blastThemAll {
   input:
   path query_file
 
-  "blastp -query ${query_file} -db nr"
+  script:
+  """
+  blastp -query ${query_file} -db nr
+  """
 }
 
 workflow {
@@ -420,26 +422,29 @@ It's worth noting that in the above example, the name of the file in the file-sy
 
 There may be cases where your task needs to use a file whose name is fixed, i.e. it does not have to change along with the actual provided file. In this case, you can specify a fixed name with the `name` attribute in the input file parameter definition, as shown in the following example:
 
-```groovy
+```nextflow
 input:
 path query_file, name: 'query.fa'
 ```
 
 or, using a shorter syntax:
 
-```groovy
+```nextflow
 input:
 path 'query.fa'
 ```
 
 The previous example can be re-written as shown below:
 
-```groovy
+```nextflow
 process blastThemAll {
   input:
   path 'query.fa'
 
-  "blastp -query query.fa -db nr"
+  script:
+  """
+  blastp -query query.fa -db nr
+  """
 }
 
 workflow {
@@ -456,11 +461,12 @@ This feature allows you to execute the process command multiple times without wo
 
 Channel factories like `Channel.fromPath` produce file objects, but a `path` input can also accept a string literal path. The string value should be an absolute path, i.e. it must be prefixed with a `/` character or a supported URI protocol (`file://`, `http://`, `s3://`, etc), and it cannot contain special characters (`\n`, etc).
 
-```groovy
+```nextflow
 process foo {
   input:
   path x
 
+  script:
   """
   your_command --in $x
   """
@@ -471,47 +477,27 @@ workflow {
 }
 ```
 
-Available options:
-
-`arity`
-: :::{versionadded} 23.09.0-edge
-  :::
-: Specify the number of expected files. Can be a number or a range:
-
-  ```groovy
-  input:
-      path('one.txt', arity: '1')         // exactly one file is expected
-      path('pair_*.txt', arity: '2')      // exactly two files are expected
-      path('many_*.txt', arity: '1..*')   // one or more files are expected
-  ```
-
-  When a task is created, Nextflow will check whether the received files for each path input match the declared arity, and fail if they do not.
-
-`stageAs`
-: Specify how the file should be named in the task work directory:
+:::{versionadded} 23.09.0-edge
+:::
 
-  ```groovy
-  process foo {
-    input:
-    path x, stageAs: 'data.txt'
+By default, `path` inputs will accept any number of files and stage them accordingly. The `arity` option can be used to enforce the expected number of files, either as a number or a range.
 
-    """
-    your_command --in data.txt
-    """
-  }
+For example:
 
-  workflow {
-    foo('/some/data/file.txt')
-  }
-  ```
+```nextflow
+input:
+    path('one.txt', arity: '1')         // exactly one file is expected
+    path('pair_*.txt', arity: '2')      // exactly two files are expected
+    path('many_*.txt', arity: '1..*')   // one or more files are expected
+```
 
-  Can be a name or a pattern as described in the [Multiple input files](#multiple-input-files) section.
+When a task is executed, Nextflow will check whether the received files for each path input match the declared arity, and fail if they do not.
 
 :::{note}
-Process `path` inputs have nearly the same interface as described in {ref}`script-file-io`, with one difference which is relevant when files are staged into a subdirectory. Given the following input:
+Process `path` inputs have nearly the same interface as described in {ref}`stdlib-types-path`, with one difference which is relevant when files are staged into a subdirectory. Given the following input:
 
-```groovy
-path x, stageAs: 'my-dir/*'
+```nextflow
+path x, name: 'my-dir/*'
 ```
 
 In this case, `x.name` returns the file name with the parent directory (e.g. `my-dir/file.txt`), whereas normally it would return the file name (e.g. `file.txt`). You can use `x.fileName.name` to get the file name.
@@ -519,16 +505,19 @@ In this case, `x.name` returns the file name with the parent directory (e.g. `my
 
 ### Multiple input files
 
-A `path` input can also accept a collection of files instead of a single value. In this case, the input variable will be a Groovy list, and you can use it as such.
+A `path` input can also accept a collection of files instead of a single value. In this case, the input variable will be a list.
 
 When the input has a fixed file name and a collection of files is received by the process, the file name will be appended with a numerical suffix representing its ordinal position in the list. For example:
 
-```groovy
+```nextflow
 process blastThemAll {
     input:
     path 'seq'
 
-    "echo seq*"
+    script:
+    """
+    echo seq*
+    """
 }
 
 workflow {
@@ -562,12 +551,15 @@ The target input file name may contain the `*` and `?` wildcards, which can be u
 
 The following example shows how a wildcard can be used in the input file definition:
 
-```groovy
+```nextflow
 process blastThemAll {
     input:
     path 'seq?.fa'
 
-    "cat seq1.fa seq2.fa seq3.fa"
+    script:
+    """
+    cat seq1.fa seq2.fa seq3.fa
+    """
 }
 
 workflow {
@@ -584,12 +576,13 @@ Rewriting input file names according to a named pattern is an extra feature and
 
 When the input file name is specified by using the `name` option or a string literal, you can also use other input values as variables in the file name string. For example:
 
-```groovy
+```nextflow
 process simpleCount {
   input:
   val x
   path "${x}.fa"
 
+  script:
   """
   cat ${x}.fa | grep '>'
   """
@@ -601,20 +594,19 @@ In the above example, the input file name is determined by the current value of
 This approach allows input files to be staged in the task directory with a name that is coherent with the current execution context.
 
 :::{tip}
-In most cases, you won't need to use dynamic file names, because each task is executed in its own directory, and input files are automatically staged into this directory by Nextflow. This behavior guarantees that input files with the same name won't overwrite each other.
-
-An example of when you may have to deal with that is when you have many input files in a task, and some of these files may have the same filename. In this case, a solution would be to use the `stageAs` option.
+In most cases, you won't need to use dynamic file names, because each task is executed in its own directory, and input files are automatically staged into this directory by Nextflow. This behavior guarantees that input files with the same name won't overwrite each other. The above example is useful specifically when there are potential file name conflicts within a single task.
 :::
 
-### Input type `env`
+### Input environment variables (`env`)
 
 The `env` qualifier allows you to define an environment variable in the process execution context based on the input value. For example:
 
-```groovy
+```nextflow
 process printEnv {
     input:
-    env HELLO
+    env 'HELLO'
 
+    script:
     '''
     echo $HELLO world!
     '''
@@ -632,15 +624,16 @@ bonjour world!
 hola world!
 ```
 
-### Input type `stdin`
+### Standard input (`stdin`)
 
 The `stdin` qualifier allows you to forward the input value to the [standard input](http://en.wikipedia.org/wiki/Standard_streams#Standard_input_.28stdin.29) of the process script. For example:
 
-```groovy
+```nextflow
 process printAll {
   input:
-  stdin str
+  stdin
 
+  script:
   """
   cat -
   """
@@ -648,7 +641,7 @@ process printAll {
 
 workflow {
   Channel.of('hello', 'hola', 'bonjour', 'ciao')
-    | map { it + '\n' }
+    | map { v -> v + '\n' }
     | printAll
 }
 ```
@@ -664,15 +657,16 @@ hello
 
 (process-input-tuple)=
 
-### Input type `tuple`
+### Input tuples (`tuple`)
 
 The `tuple` qualifier allows you to group multiple values into a single input definition. It can be useful when a channel emits tuples of values that need to be handled separately. Each element in the tuple is associated with a corresponding element in the `tuple` definition. For example:
 
-```groovy
+```nextflow
 process tupleExample {
     input:
     tuple val(x), path('input.txt')
 
+    script:
     """
     echo "Processing $x"
     cat input.txt > copy
@@ -692,12 +686,13 @@ A `tuple` definition may contain any of the following qualifiers, as previously
 
 The `each` qualifier allows you to repeat the execution of a process for each item in a collection, each time a new value is received. For example:
 
-```groovy
+```nextflow
 process alignSequences {
   input:
   path seq
   each mode
 
+  script:
   """
   t_coffee -in $seq -mode $mode > result
   """
@@ -715,13 +710,14 @@ In the above example, each time a file of sequences is emitted from the `sequenc
 
 Input repeaters can be applied to files as well. For example:
 
-```groovy
+```nextflow
 process alignSequences {
   input:
   path seq
   each mode
   each path(lib)
 
+  script:
   """
   t_coffee -in $seq -mode $mode -lib $lib > result
   """
@@ -758,7 +754,7 @@ As a result, channel values are consumed sequentially and any empty channel will
 
 For example:
 
-```groovy
+```nextflow
 process foo {
   input:
   val x
@@ -788,7 +784,7 @@ A different semantic is applied when using a {ref}`value channel <channel-type-v
 
 To better understand this behavior, compare the previous example with the following one:
 
-```groovy
+```nextflow
 process bar {
   input:
   val x
@@ -841,18 +837,19 @@ When a process is invoked, each process output is returned as a channel. The exa
 The following output qualifiers are available:
 
 - `val`: Emit the variable with the specified name.
-- `file`: (DEPRECATED) Emit a file produced by the process with the specified name.
 - `path`: Emit a file produced by the process with the specified name.
 - `env`: Emit the variable defined in the process environment with the specified name.
 - `stdout`: Emit the `stdout` of the executed process.
 - `tuple`: Emit multiple values.
 - `eval`: Emit the result of a script or command evaluated in the task execution context.
 
-### Output type `val`
+Refer to the {ref}`process reference <process-reference-outputs>` for the full list of available output methods and options.
+
+### Output variables (`val`)
 
 The `val` qualifier allows you to output any Nextflow variable defined in the process. A common use case is to output a variable that was defined in the `input` block, as shown in the following example:
 
-```groovy
+```nextflow
 process foo {
   input:
   each x
@@ -860,6 +857,7 @@ process foo {
   output:
   val x
 
+  script:
   """
   echo $x > file
   """
@@ -869,13 +867,13 @@ workflow {
   methods = ['prot', 'dna', 'rna']
 
   receiver = foo(methods)
-  receiver.view { "Received: $it" }
+  receiver.view { method -> "Received: $method" }
 }
 ```
 
 The output value can be a value literal, an input variable, any other Nextflow variable in the process scope, or a value expression. For example:
 
-```groovy
+```nextflow
 process foo {
   input:
   path infile
@@ -896,29 +894,22 @@ workflow {
   ch_dummy = Channel.fromPath('*').first()
   (ch_var, ch_str, ch_exp) = foo(ch_dummy)
 
-  ch_var.view { "ch_var: $it" }
-  ch_str.view { "ch_str: $it" }
-  ch_exp.view { "ch_exp: $it" }
+  ch_var.view { var -> "ch_var: $var" }
+  ch_str.view { str -> "ch_str: $str" }
+  ch_exp.view { exp -> "ch_exp: $exp" }
 }
 ```
 
-### Output type `file`
-
-:::{note}
-The `file` qualifier was the standard way to handle input files prior to Nextflow 19.10.0. In later versions of Nextflow, the `path` qualifier should be preferred over `file`.
-:::
-
-The `file` qualifier is similar to `path`, but with some differences. The `file` qualifier interprets `:` as a path separator, therefore `file 'foo:bar'` captures two files named `foo` and `bar`, whereas `path 'foo:bar'` captures a single file named `foo:bar`. Additionally, `file` does not support all of the extra options provided by `path`.
-
-### Output type `path`
+### Output files (`path`)
 
 The `path` qualifier allows you to output one or more files produced by the process. For example:
 
-```groovy
+```nextflow
 process randomNum {
   output:
   path 'result.txt'
 
+  script:
   '''
   echo $RANDOM > result.txt
   '''
@@ -926,66 +917,49 @@ process randomNum {
 
 workflow {
   numbers = randomNum()
-  numbers.view { "Received: ${it.text}" }
+  numbers.view { file -> "Received: ${file.text}" }
 }
 ```
 
 In the above example, the `randomNum` process creates a file named `result.txt` which contains a random number. Since a `path` output with the same name is declared, that file is emitted by the corresponding output channel. A downstream process with a compatible input channel will be able to receive it.
 
-Available options:
-
-`arity`
-: :::{versionadded} 23.09.0-edge
-  :::
-: Specify the number of expected files. Can be a number or a range:
-
-  ```groovy
-  output:
-      path('one.txt', arity: '1')         // exactly one file is expected
-      path('pair_*.txt', arity: '2')      // exactly two files are expected
-      path('many_*.txt', arity: '1..*')   // one or more files are expected
-  ```
-
-  When a task completes, Nextflow will check whether the produced files for each path output match the declared arity,
-  and fail if they do not. If the arity is `1`, a sole file object will be emitted. Otherwise, a list will always be emitted,
-  even if only one file is produced.
-
-`followLinks`
-: When `true`, target files are returned in place of any matching symlink (default: `true`)
+Refer to the {ref}`process reference <process-reference-outputs>` for the list of available options for `path` outputs.
 
-`glob`
-: When `true`, the specified name is interpreted as a glob pattern (default: `true`)
+:::{versionadded} 23.09.0-edge
+:::
 
-`hidden`
-: When `true`, hidden files are included in the matching output files (default: `false`)
+By default, `path` outputs will accept any number of matching files from the task directory. The `arity` option can be used to enforce the expected number of files, either as a number or a range.
 
-`includeInputs`
-: When `true` and the output path is a glob pattern, any input files matching the pattern are also included in the output (default: `false`)
+For example:
 
-`maxDepth`
-: Maximum number of directory levels to visit (default: no limit).
+```nextflow
+output:
+path('one.txt', arity: '1')         // exactly one file is expected
+path('pair_*.txt', arity: '2')      // exactly two files are expected
+path('many_*.txt', arity: '1..*')   // one or more files are expected
+```
 
-`type`
-: Type of paths returned, either `file`, `dir` or `any` (default: `any`, or `file` if the specified file name pattern contains a double star (`**`))
+When a task completes, Nextflow will check whether the produced files for each path output match the declared arity, and fail if they do not.
 
 ### Multiple output files
 
 When an output file name contains a `*` or `?` wildcard character, it is interpreted as a [glob][glob] path matcher. This allows you to capture multiple files into a list and emit the list as a single value. For example:
 
-```groovy
+```nextflow
 process splitLetters {
     output:
     path 'chunk_*'
 
-    '''
+    script:
+    """
     printf 'Hola' | split -b 1 - chunk_
-    '''
+    """
 }
 
 workflow {
     splitLetters
         | flatten
-        | view { "File: ${it.name} => ${it.text}" }
+        | view { chunk -> "File: ${chunk.name} => ${chunk.text}" }
 }
 ```
 
@@ -1015,7 +989,7 @@ Read more about glob syntax at the following link [What is a glob?][glob]
 
 When an output file name needs to be expressed dynamically, it is possible to define it using a dynamic string which references variables in the `input` block or in the script global context. For example:
 
-```groovy
+```nextflow
 process align {
   input:
   val species
@@ -1024,6 +998,7 @@ process align {
   output:
   path "${species}.aln"
 
+  script:
   """
   t_coffee -in $seq > ${species}.aln
   """
@@ -1046,31 +1021,27 @@ To sum up, the use of output files with static names over dynamic ones is prefer
 
 (process-env)=
 
-### Output type `env`
+### Output environment variables (`env`)
 
 The `env` qualifier allows you to output a variable defined in the process execution environment:
 
 ```{literalinclude} snippets/process-out-env.nf
-:language: groovy
+:language: nextflow
 ```
 
-:::{versionchanged} 23.12.0-edge
-Prior to this version, if the environment variable contained multiple lines of output, the output would be compressed to a single line by converting newlines to spaces.
-:::
-
 (process-stdout)=
 
-### Output type `stdout`
+### Standard output (`stdout`)
 
 The `stdout` qualifier allows you to output the `stdout` of the executed process:
 
 ```{literalinclude} snippets/process-stdout.nf
-:language: groovy
+:language: nextflow
 ```
 
 (process-out-eval)=
 
-### Output type `eval`
+### Eval output (`eval`)
 
 :::{versionadded} 24.02.0-edge
 :::
@@ -1078,7 +1049,7 @@ The `stdout` qualifier allows you to output the `stdout` of the executed process
 The `eval` qualifier allows you to capture the standard output of an arbitrary command evaluated the task shell interpreter context:
 
 ```{literalinclude} snippets/process-out-eval.nf
-:language: groovy
+:language: nextflow
 ```
 
 Only one-line Bash commands are supported. You can use a semi-colon `;` to specify multiple Bash commands on a single line, and many interpreters can execute arbitrary code on the command line, e.g. `python -c 'print("Hello world!")'`.
@@ -1087,11 +1058,11 @@ If the command fails, the task will also fail. In Bash, you can append `|| true`
 
 (process-out-tuple)=
 
-### Output type `tuple`
+### Output tuples (`tuple`)
 
 The `tuple` qualifier allows you to output multiple values in a single channel. It is useful when you need to associate outputs with metadata, for example:
 
-```groovy
+```nextflow
 process blast {
   input:
     val species
@@ -1107,7 +1078,7 @@ process blast {
 }
 
 workflow {
-  ch_species = Channel.from('human', 'cow', 'horse')
+  ch_species = Channel.of('human', 'cow', 'horse')
   ch_query = Channel.fromPath('*.fa')
 
   blast(ch_species, ch_query)
@@ -1123,93 +1094,89 @@ While parentheses for input and output qualifiers are generally optional, they a
 
 Here's an example with a single path output (parentheses optional):
 
-```groovy
+```nextflow
 process foo {
     output:
     path 'result.txt', hidden: true
 
-    '''
+    script:
+    """
     echo 'another new line' >> result.txt
-    '''
+    """
 }
 ```
 
 And here's an example with a tuple output (parentheses required):
 
-```groovy
+```nextflow
 process foo {
     output:
     tuple path('last_result.txt'), path('result.txt', hidden: true)
 
-    '''
+    script:
+    """
     echo 'another new line' >> result.txt
     echo 'another new line' > last_result.txt
-    '''
+    """
 }
 ```
 :::
 
-(process-additional-options)=
-
-### Additional options
-
-The following options are available for all process outputs:
-
-`emit: <name>`
+(process-naming-outputs)=
 
-: Defines the name of the output channel, which can be used to access the channel by name from the process output:
+### Naming outputs
 
-  ```groovy
-  process FOO {
-      output:
-      path 'hello.txt', emit: hello
-      path 'bye.txt', emit: bye
+The `emit` option can be used on a process output to define a name for the corresponding output channel, which can be used to access the channel by name from the process output. For example:
 
-      """
-      echo "hello" > hello.txt
-      echo "bye" > bye.txt
-      """
-  }
-
-  workflow {
-      FOO()
-      FOO.out.hello.view()
-  }
-  ```
-
-  See {ref}`workflow-process-invocation` for more details.
+```nextflow
+process FOO {
+    output:
+    path 'hello.txt', emit: hello
+    path 'bye.txt', emit: bye
 
-`optional: true | false`
+    script:
+    """
+    echo "hello" > hello.txt
+    echo "bye" > bye.txt
+    """
+}
 
-: Normally, if a specified output is not produced by the task, the task will fail. Setting `optional: true` will cause the task to not fail, and instead emit nothing to the given output channel.
+workflow {
+    FOO()
+    FOO.out.hello.view()
+}
+```
 
-  ```groovy
-  output:
-  path("output.txt"), optional: true
-  ```
+See {ref}`workflow-process-invocation` for more details.
 
-  In this example, the process is normally expected to produce an `output.txt` file, but in the cases where the file is missing, the task will not fail. The output channel will only contain values for those tasks that produced `output.txt`.
+### Optional outputs
 
-: :::{note}
-  While this option can be used with any process output, it cannot be applied to individual elements of a [tuple](#output-type-tuple) output. The entire tuple must be optional or not optional.
-  :::
+Normally, if a specified output is not produced by the task, the task will fail. Setting `optional: true` will cause the task to not fail, and instead emit nothing to the given output channel.
 
-`topic: <name>`
+```nextflow
+output:
+path("output.txt"), optional: true
+```
 
-: :::{versionadded} 23.11.0-edge
-  :::
+In this example, the process is normally expected to produce an `output.txt` file, but in this case, if the file is missing, the task will not fail. The output channel will only contain values for those tasks that produced `output.txt`.
 
-: *Experimental: may change in a future release.*
+:::{note}
+While this option can be used with any process output, it cannot be applied to individual elements of a [tuple](#output-tuples-tuple) output. The entire tuple must be optional or not optional.
+:::
 
-: Defines the {ref}`channel topic <channel-topic>` to which the output will be sent.
+(process-when)=
 
 ## When
 
+:::{deprecated} 24.10.0
+Use conditional logic (e.g. `if` statement, {ref}`operator-filter` operator) in the calling workflow instead.
+:::
+
 The `when` block allows you to define a condition that must be satisfied in order to execute the process. The condition can be any expression that returns a boolean value.
 
 It can be useful to enable/disable the process execution depending on the state of various inputs and parameters. For example:
 
-```groovy
+```nextflow
 process find {
   input:
   path proteins
@@ -1225,1572 +1192,151 @@ process find {
 }
 ```
 
-:::{tip}
-As a best practice, it is better to define such control flow logic in the workflow block, i.e. with an `if` statement or with channel operators, to make the process more portable.
-:::
-
 (process-directives)=
 
 ## Directives
 
 Directives are optional settings that affect the execution of the current process.
 
-They must be entered at the top of the process body, before any other declaration blocks (`input`, `output`, etc), and have the following syntax:
-
-```groovy
-// directive with simple value
-name value
-
-// directive with list value
-name arg1, arg2, arg3
-
-// directive with map value
-name key1: val1, key2: val2
+By default, directives are evaluated when the process is defined. However, if the value is a dynamic string or closure, it will be evaluated separately for each task, which allows task-specific variables like `task` and `val` inputs to be used.
 
-// directive with value and options
-name arg, opt1: val1, opt2: val2
-```
+Some directives are only supported by specific executors. Refer to the {ref}`executor-page` page for more information about each executor.
 
-By default, directives are evaluated when the process is defined. However, if the value is a dynamic string or closure, it will be evaluated separately for each task, which allows task-specific variables like `task` and `val` inputs to be used.
+Refer to the {ref}`process reference <process-reference-directives>` for the full list of process directives. If you are new to Nextflow, here are some commonly-used operators to learn first:
 
-Some directives are generally available to all processes, while others depend on the `executor` currently defined.
+General:
+- {ref}`process-error-strategy`: strategy for handling task failures
+- {ref}`process-executor`: the {ref}`executor <executor-page>` with which to execute tasks
+- {ref}`process-tag`: a semantic name used to differentiate between task executions of the same process
 
-(process-accelerator)=
+Resource requirements:
+- {ref}`process-cpus`: the number of CPUs to request for each task
+- {ref}`process-memory`: the amount of memory to request for each task
+- {ref}`process-time`: the amount of walltime to request for each task
 
-### accelerator
+Software dependencies:
+- {ref}`process-conda`: list of conda packages to provision for tasks
+- {ref}`process-container`: container image to use for tasks
 
-:::{versionadded} 19.09.0-edge
-:::
+### Using task directive values
 
-The `accelerator` directive allows you to request hardware accelerators (e.g. GPUs) for the task execution. For example:
+The `task` object also contains the values of all process directives for the given task, which allows you to access these settings at runtime. For examples:
 
-```groovy
+```nextflow
 process foo {
-    accelerator 4, type: 'nvidia-tesla-k80'
-
-    script:
-    """
-    your_gpu_enabled --command --line
-    """
+  script:
+  """
+  some_tool --cpus $task.cpus --mem $task.memory
+  """
 }
 ```
 
-The above examples will request 4 GPUs of type `nvidia-tesla-k80`.
-
-:::{note}
-This directive is only used by certain executors. Refer to the {ref}`executor-page` page to see which executors support this directive.
-:::
-
-:::{note}
-The accelerator `type` option depends on the target execution platform. Refer to the platform-specific documentation for details on the available accelerators:
-
-- [Google Cloud](https://cloud.google.com/compute/docs/gpus/)
-- [Kubernetes](https://kubernetes.io/docs/tasks/manage-gpus/scheduling-gpus/#clusters-containing-different-types-of-gpus)
+In the above snippet, `task.cpus` and `task.memory` hold the values for the {ref}`cpus directive<process-cpus>` and {ref}`memory directive<process-memory>` directives, respectively, which were resolved for this task based on the process configuration.
 
-The accelerator `type` option is not supported for AWS Batch. You can control the accelerator type indirectly through the allowed instance types in your Compute Environment. See the [AWS Batch FAQs](https://aws.amazon.com/batch/faqs/?#GPU_Scheduling_) for more information.
-:::
-
-(process-afterscript)=
-
-### afterScript
-
-The `afterScript` directive allows you to execute a custom (Bash) snippet immediately *after* the main process has run. This may be useful to clean up your staging area.
+(dynamic-directives)=
 
-:::{note}
-When combined with the {ref}`container directive <process-container>`, the `afterScript` will be executed outside the specified container. In other words, the `afterScript` is always executed in the host environment.
-:::
+### Dynamic directives
 
-(process-arch)=
+A directive can be assigned *dynamically*, during the process execution, so that its actual value can be evaluated based on the process inputs.
 
-### arch
+To be defined dynamically, the directive's value needs to be expressed using a {ref}`closure <script-closure>`. For example:
 
-The `arch` directive allows you to define the CPU architecture to build the software in use by the process' task. For example:
+```nextflow
+process foo {
+  executor 'sge'
+  queue { entries > 100 ? 'long' : 'short' }
 
-```groovy
-process cpu_task {
-    spack 'blast-plus@2.13.0'
-    arch 'linux/x86_64', target: 'cascadelake'
+  input:
+  tuple val(entries), path('data.txt')
 
-    """
-    blastp -query input_sequence -num_threads ${task.cpus}
-    """
+  script:
+  """
+  your_command --here
+  """
 }
 ```
 
-The example above declares that the CPU generic architecture is `linux/x86_64` (X86 64 bit), and more specifically that the microarchitecture is `cascadelake` (a specific generation of Intel CPUs).
-
-This directive is currently used by the following Nextflow functionalities:
-
-- by the [spack](#spack) directive, to build microarchitecture-optimised applications;
-- by the {ref}`wave-page` service, to build containers for one of the generic families of CPU architectures (see below);
-- by the `spack` strategy within {ref}`wave-page`, to optimise the container builds for specific CPU microarchitectures.
-
-Allowed values for the `arch` directive are as follows, grouped by equivalent family (choices available for the sake of compatibility):
-- X86 64 bit: `linux/x86_64`, `x86_64`, `linux/amd64`, `amd64`
-- ARM 64 bit: `linux/aarch64`, `aarch64`, `linux/arm64`, `arm64`, `linux/arm64/v8`
-- ARM 64 bit, older generation: `linux/arm64/v7`
-
-Examples of values for the architecture `target` option are `cascadelake`, `icelake`, `zen2` and `zen3`. See the Spack documentation for the full and up-to-date [list of meaningful targets](https://spack.readthedocs.io/en/latest/basic_usage.html#support-for-specific-microarchitectures).
-
-(process-array)=
+In the above example, the {ref}`process-queue` directive is evaluated dynamically, depending on the input value `entries`. When it is larger than 100, jobs will be submitted to the `long` queue, otherwise the `short` queue will be used.
 
-### array
-
-:::{versionadded} 24.04.0
-:::
-
-:::{warning} *Experimental: may change in a future release.*
-:::
-
-The `array` directive allows you to submit tasks as *job arrays* for executors that support it.
-
-A job array is a collection of jobs with the same resource requirements and the same script (parameterized by an index). Job arrays incur significantly less scheduling overhead compared to individual jobs, and as a result they are preferred by HPC schedulers where possible.
+All directives can be assigned a dynamic value except the following:
 
-The directive should be specified with a given array size, along with an executor that supports job arrays. For example:
+- {ref}`process-executor`
+- {ref}`process-label`
+- {ref}`process-maxforks`
 
-```groovy
-process cpu_task {
-    executor 'slurm'
-    array 100
+:::{tip}
+Assigning a string value with one or more variables is always resolved in a dynamic manner, and therefore is equivalent to the above syntax. For example, the above directive can also be written as:
 
-    '''
-    your_command --here
-    '''
-}
+```nextflow
+queue "${ entries > 100 ? 'long' : 'short' }"
 ```
 
-Nextflow currently supports job arrays for the following executors:
-
-- {ref}`awsbatch-executor`
-- {ref}`google-batch-executor`
-- {ref}`lsf-executor`
-- {ref}`pbs-executor`
-- {ref}`pbspro-executor`
-- {ref}`sge-executor`
-- {ref}`slurm-executor`
-
-A process using job arrays will collect tasks and submit each batch as a job array when it is ready. Any "leftover" tasks will be submitted as a partial job array.
-
-Once a job array is submitted, each "child" task is executed as an independent job. Any tasks that fail (and can be retried) will be retried without interfering with the tasks that succeeded. Retried tasks are submitted individually rather than through a job array, in order to allow for the use of [dynamic resources](#dynamic-computing-resources).
-
-The following directives must be uniform across all tasks in a process that uses job arrays, because these directives are specified once for the entire job array:
-
-- {ref}`process-accelerator`
-- {ref}`process-clusterOptions`
-- {ref}`process-cpus`
-- {ref}`process-disk`
-- {ref}`process-machineType`
-- {ref}`process-memory`
-- {ref}`process-queue`
-- {ref}`process-resourcelabels`
-- {ref}`process-resourcelimits`
-- {ref}`process-time`
-
-For cloud-based executors like AWS Batch, or when using Fusion with any executor, the following additional directives must be uniform:
-
-- {ref}`process-container`
-- {ref}`process-containerOptions`
+Note, however, that the latter syntax can be used both for a directive's main argument (as in the above example) and for a directive's optional named attributes, whereas the closure syntax is only resolved dynamically for a directive's main argument.
+:::
 
-(process-beforescript)=
+(dynamic-task-resources)=
 
-### beforeScript
+### Dynamic task resources
 
-The `beforeScript` directive allows you to execute a custom (Bash) snippet *before* the main process script is run. This may be useful to initialise the underlying cluster environment or for other custom initialisation.
+It's a very common scenario that different instances of the same process may have very different needs in terms of computing resources. In such situations requesting, for example, an amount of memory too low will cause some tasks to fail. Instead, using a higher limit that fits all the tasks in your execution could significantly decrease the execution priority of your jobs.
 
-For example:
+The [Dynamic directives](#dynamic-directives) evaluation feature can be used to modify the amount of computing resources requested in case of a process failure and try to re-execute it using a higher limit. For example:
 
-```groovy
+```nextflow
 process foo {
-  beforeScript 'source /cluster/bin/setup'
-
-  """
-  echo bar
-  """
-}
-```
-
-When the process is containerized (using the {ref}`process-container` directive), the `beforeScript` will be executed in the container only if the executor is *container-native* (e.g. cloud batch executors, Kubernetes). Otherwise, the `beforeScript` will be executed outside the container.
-
-(process-cache)=
-
-### cache
-
-The `cache` directive allows you to store the process results to a local cache. When the cache is enabled *and* the pipeline is launched with the {ref}`resume <getstarted-resume>` option, any task executions that are already cached will be re-used. See the {ref}`cache-resume-page` page for more information about how the cache works.
-
-The cache is enabled by default, but you can disable it for a specific process by setting the `cache` directive to `false`. For example:
+    memory { 2.GB * task.attempt }
+    time { 1.hour * task.attempt }
 
-```groovy
-process noCacheThis {
-  cache false
+    errorStrategy { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+    maxRetries 3
 
-  script:
-  <your command string here>
+    script:
+    """
+    your_command --here
+    """
 }
 ```
 
-The following options are available:
-
-`false`
-: Disable caching.
-
-`true` (default)
-: Enable caching. Input file metadata (name, size, last updated timestamp) are included in the cache keys.
-
-`'deep'`
-: Enable caching. Input file content is included in the cache keys.
+In the above example the {ref}`process-memory` and execution {ref}`process-time` limits are defined dynamically. The first time the process is executed the `task.attempt` is set to `1`, thus it will request a two GB of memory and one hour of maximum execution time.
 
-`'lenient'`
-: Enable caching. Minimal input file metadata (name and size only) are included in the cache keys.
-: This strategy provides a workaround for incorrect caching invalidation observed on shared file systems due to inconsistent file timestamps.
-
-(process-clusteroptions)=
-
-### clusterOptions
-
-The `clusterOptions` directive allows the usage of any native configuration option accepted by your cluster submit command. You can use it to request non-standard resources or use settings that are specific to your cluster and not supported out of the box by Nextflow.
-
-The cluster options can be a string:
+If the task execution fail reporting an exit status in the range between 137 and 140, the task is re-submitted (otherwise terminates immediately). This time the value of `task.attempt` is `2`, thus increasing the amount of the memory to four GB and the time to 2 hours, and so on.
 
-```groovy
-process foo {
-  clusterOptions '-x 1 -y 2'
-  // ...
-}
-```
+The directive {ref}`process-maxretries` set the maximum number of time the same task can be re-executed.
 
-:::{versionchanged} 24.04.0
-Prior to this version, grid executors that require each option to be on a separate line in the job script would attempt to split multiple options using a variety of different conventions. Multiple options can now be specified more clearly using a string list as shown below.
+### Dynamic task resources with previous execution trace
+:::{versionadded} 24.10.0
 :::
 
-The cluster options can also be a string list:
+Task resource requests can be updated relative to the {ref}`trace record <trace-report>` metrics of the previous task attempt. The metrics can be accessed through the `task.previousTrace` variable. For example:
 
-```groovy
+```nextflow
 process foo {
-  clusterOptions '-x 1', '-y 2', '--flag'
-  // ...
+    memory { task.attempt > 1 ? task.previousTrace.memory * 2 : (1.GB) }
+    errorStrategy { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+    maxRetries 3
+
+    script:
+    """
+    your_command --here
+    """
 }
 ```
+In the above example, the {ref}`process-memory` is set according to previous trace record metrics. In the first attempt, when no trace metrics are available, it is set to one GB. In the subsequent attempts, it doubles the previously allocated memory. See {ref}`trace-report` for more information about trace records.
 
-Grid executors that require one option per line will write each option to a separate line, while grid executors that allow multiple options per line will write all options to a single line, the same as with a string. This form is useful to control how the options are split across lines when it is required by the scheduler.
-
-:::{note}
-This directive is only used by grid executors. Refer to the {ref}`executor-page` page to see which executors support this directive.
-:::
-
-:::{warning}
-While you can use the `clusterOptions` directive to specify options that are supported as process directives (`queue`, `memory`, `time`, etc), you should not use both at the same time, as it will cause undefined behavior. Most HPC schedulers will either fail or simply ignore one or the other.
-:::
-
-(process-conda)=
 
-### conda
+### Dynamic retry with backoff
 
-The `conda` directive allows for the definition of the process dependencies using the [Conda](https://conda.io) package manager.
-
-Nextflow automatically sets up an environment for the given package names listed by in the `conda` directive. For example:
+There are cases in which the required execution resources may be temporary unavailable e.g. network congestion. In these cases immediately re-executing the task will likely result in the identical error. A retry with an exponential backoff delay can better recover these error conditions:
 
-```groovy
+```nextflow
 process foo {
-  conda 'bwa=0.7.15'
+  errorStrategy { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
+  maxRetries 5
 
-  '''
+  script:
+  """
   your_command --here
-  '''
-}
-```
-
-Multiple packages can be specified separating them with a blank space e.g. `bwa=0.7.15 fastqc=0.11.5`. The name of the channel from where a specific package needs to be downloaded can be specified using the usual Conda notation i.e. prefixing the package with the channel name as shown here `bioconda::bwa=0.7.15`.
-
-The `conda` directive also allows the specification of a Conda environment file path or the path of an existing environment directory. See the {ref}`conda-page` page for further details.
-
-(process-container)=
-
-### container
-
-The `container` directive allows you to execute the process script in a [Docker](http://docker.io) container.
-
-It requires the Docker daemon to be running in machine where the pipeline is executed, i.e. the local machine when using the *local* executor or the cluster nodes when the pipeline is deployed through a *grid* executor.
-
-For example:
-
-```groovy
-process runThisInDocker {
-  container 'dockerbox:tag'
-
-  """
-  <your holy script here>
-  """
-}
-```
-
-Simply replace in the above script `dockerbox:tag` with the name of the Docker image you want to use.
-
-:::{tip}
-Containers are a very useful way to execute your scripts in a reproducible self-contained environment or to run your pipeline in the cloud.
-:::
-
-:::{note}
-This directive is ignored for processes that are {ref}`executed natively <process-native>`.
-:::
-
-(process-containeroptions)=
-
-### containerOptions
-
-The `containerOptions` directive allows you to specify any container execution option supported by the underlying container engine (ie. Docker, Singularity, etc). This can be useful to provide container settings only for a specific process e.g. mount a custom path:
-
-```groovy
-process runThisWithDocker {
-    container 'busybox:latest'
-    containerOptions '--volume /data/db:/db'
-
-    output:
-    path 'output.txt'
-
-    '''
-    your_command --data /db > output.txt
-    '''
-}
-```
-
-:::{warning}
-This feature is not supported by the {ref}`k8s-executor` and {ref}`google-lifesciences-executor` executors.
-:::
-
-(process-cpus)=
-
-### cpus
-
-The `cpus` directive allows you to define the number of (logical) CPU required by the process' task. For example:
-
-```groovy
-process big_job {
-  cpus 8
-  executor 'sge'
-
-  """
-  blastp -query input_sequence -num_threads ${task.cpus}
-  """
-}
-```
-
-This directive is required for tasks that execute multi-process or multi-threaded commands/tools and it is meant to reserve enough CPUs when a pipeline task is executed through a cluster resource manager.
-
-See also: [penv](#penv), [memory](#memory), [time](#time), [queue](#queue), [maxForks](#maxforks)
-
-(process-debug)=
-
-### debug
-
-By default the `stdout` produced by the commands executed in all processes is ignored. By setting the `debug` directive to `true`, you can forward the process `stdout` to the current top running process `stdout` file, showing it in the shell terminal.
-
-For example:
-
-```groovy
-process sayHello {
-  debug true
-
-  script:
-  "echo Hello"
-}
-```
-
-```
-Hello
-```
-
-Without specifying `debug true`, you won't see the `Hello` string printed out when executing the above example.
-
-(process-disk)=
-
-### disk
-
-The `disk` directive allows you to define how much local disk storage the process is allowed to use. For example:
-
-```groovy
-process big_job {
-    disk '2 GB'
-    executor 'cirrus'
-
-    """
-    your task script here
-    """
-}
-```
-
-The following memory unit suffix can be used when specifying the disk value:
-
-| Unit | Description |
-| ---- | ----------- |
-| B    | Bytes       |
-| KB   | Kilobytes   |
-| MB   | Megabytes   |
-| GB   | Gigabytes   |
-| TB   | Terabytes   |
-
-See {ref}`implicit-classes-memoryunit` for more information.
-
-:::{note}
-This directive is only used by certain executors. Refer to the {ref}`executor-page` page to see which executors support this directive.
-:::
-
-See also: [cpus](#cpus), [memory](#memory) [time](#time), [queue](#queue) and [Dynamic computing resources](#dynamic-computing-resources).
-
-(process-echo)=
-
-### echo
-
-:::{deprecated} 22.04.0
-Use `debug` instead
-:::
-
-(process-error-strategy)=
-
-### errorStrategy
-
-The `errorStrategy` directive allows you to define how an error condition is managed by the process. By default when an error status is returned by the executed script, the process stops immediately. This in turn forces the entire pipeline to terminate.
-
-The following error strategies are available:
-
-`terminate` (default)
-: When a task fails, terminate the pipeline immediately. Pending and running jobs are killed.
-
-`finish`
-: When a task fails, wait for submitted and running tasks to finish and then terminate the pipeline.
-
-`ignore`
-: Ignore all task failures and complete the pipeline execution successfully.
-: :::{versionadded} 24.05.0-edge
-  When the `workflow.failOnIgnore` config option is set to `true`, the pipeline will return a non-zero exit code if one or more failed tasks were ignored.
-  :::
-
-`retry`
-: When a task fails, retry it.
-
-When setting the `errorStrategy` directive to `ignore` the process doesn't stop on an error condition, it just reports a message notifying you of the error event.
-
-For example:
-
-```groovy
-process ignoreAnyError {
-  errorStrategy 'ignore'
-
-  script:
-  <your command string here>
-}
-```
-
-:::{note}
-By definition, a command script fails when it ends with a non-zero exit status.
-:::
-
-:::{tip}
-To illustrate the differences between error strategies, consider the following example. Let's say you are analyzing 96 patient samples and the data from one is corrupted, causing the associated task to fail. The different ways to handle this failure are as follows:
-
-- **errorStrategy `terminate`**: Nextflow will cancel any other ongoing tasks at the time of the failure, exit the pipeline, and report an error.
-- **errorStrategy `finish`**: Nextflow will allow any other existing tasks to conclude (but not submit any more) and report an error.
-- **errorStrategy `ignore`**: Nextflow will continue submitting tasks for the remaining 95 samples, complete the workflow, and report a successful pipeline completion.
-- **errorStrategy `ignore` and `workflow.failOnIgnore` set to `true` in configuration**: The same behavior as setting the errorStrategy alone, except the pipeline will return an exit status of -1 and report an error.
-
-See {ref}`metadata-workflow` for more information on `workflow.failOnIgnore`.
-:::
-
-The `retry` error strategy allows you to re-submit for execution a process returning an error condition. For example:
-
-```groovy
-process retryIfFail {
-  errorStrategy 'retry'
-
-  script:
-  <your command string here>
-}
-```
-
-The number of times a failing process is re-executed is defined by the [maxRetries](#maxretries) and [maxErrors](#maxerrors) directives.
-
-:::{tip}
-More complex strategies depending on the task exit status or other parametric values can be defined using a dynamic `errorStrategy`. See the [Dynamic directives](#dynamic-directives) section for details.
-:::
-
-See also: [maxErrors](#maxerrors), [maxRetries](#maxretries) and [Dynamic computing resources](#dynamic-computing-resources).
-
-(process-executor)=
-
-### executor
-
-The `executor` defines the underlying system where processes are executed. By default a process uses the executor defined globally in the `nextflow.config` file.
-
-The `executor` directive allows you to configure what executor has to be used by the process, overriding the default configuration.
-
-The following executors are available:
-
-| Name                  | Executor                                                                                    |
-| --------------------- | ------------------------------------------------------------------------------------------- |
-| `awsbatch`            | [AWS Batch](https://aws.amazon.com/batch/) service                                          |
-| `azurebatch`          | [Azure Batch](https://azure.microsoft.com/en-us/services/batch/) service                    |
-| `condor`              | [HTCondor](https://research.cs.wisc.edu/htcondor/) job scheduler                            |
-| `google-lifesciences` | [Google Genomics Pipelines](https://cloud.google.com/life-sciences) service                 |
-| `k8s`                 | [Kubernetes](https://kubernetes.io/) cluster                                                |
-| `local`               | The computer where `Nextflow` is launched                                                   |
-| `lsf`                 | [Platform LSF](http://en.wikipedia.org/wiki/Platform_LSF) job scheduler                     |
-| `moab`                | [Moab](http://www.adaptivecomputing.com/moab-hpc-basic-edition/) job scheduler              |
-| `nqsii`               | [NQSII](https://www.rz.uni-kiel.de/en/our-portfolio/hiperf/nec-linux-cluster) job scheduler |
-| `oge`                 | Alias for the `sge` executor                                                                |
-| `pbs`                 | [PBS/Torque](http://en.wikipedia.org/wiki/Portable_Batch_System) job scheduler              |
-| `pbspro`              | [PBS Pro](https://www.pbsworks.com/) job scheduler                                          |
-| `sge`                 | Sun Grid Engine / [Open Grid Engine](http://gridscheduler.sourceforge.net/)                 |
-| `slurm`               | [SLURM](https://en.wikipedia.org/wiki/Slurm_Workload_Manager) workload manager              |
-| `uge`                 | Alias for the `sge` executor                                                                |
-
-The following example shows how to set the process's executor:
-
-```groovy
-process doSomething {
-  executor 'sge'
-
-  script:
-  <your script here>
-}
-```
-
-:::{note}
-Each executor supports additional directives and `executor` configuration options. Refer to the {ref}`executor-page` page to see what each executor supports.
-:::
-
-(process-ext)=
-
-### ext
-
-The `ext` is a special directive used as *namespace* for user custom process directives. This can be useful for advanced configuration options. For example:
-
-```groovy
-process mapping {
-  container "biocontainers/star:${task.ext.version}"
-
-  input:
-  path genome
-  tuple val(sampleId), path(reads)
-
-  """
-  STAR --genomeDir $genome --readFilesIn $reads ${task.ext.args ?: ''}
-  """
-}
-```
-
-In the above example, the process container version is controlled by `ext.version`, and the script supports additional command line arguments through `ext.args`.
-
-The `ext` directive can be set in the process definition:
-
-```groovy
-process mapping {
-  ext version: '2.5.3', args: '--foo --bar'
-}
-```
-
-Or in the Nextflow configuration:
-
-```groovy
-process.ext.version = '2.5.3'
-process.ext.args = '--foo --bar'
-```
-
-(process-fair)=
-
-### fair
-
-:::{versionadded} 22.12.0-edge
-:::
-
-The `fair` directive, when enabled, guarantees that process outputs will be emitted in the order in which they were received. For example:
-
-```groovy
-process foo {
-    fair true
-
-    input:
-    val x
-    output:
-    tuple val(task.index), val(x)
-
-    script:
-    """
-    sleep \$((RANDOM % 3))
-    """
-}
-
-workflow {
-    channel.of('A','B','C','D') | foo | view
-}
-```
-
-The above example produces:
-
-```
-[1, A]
-[2, B]
-[3, C]
-[4, D]
-```
-
-(process-label)=
-
-### label
-
-The `label` directive allows the annotation of processes with mnemonic identifier of your choice. For example:
-
-```groovy
-process bigTask {
-  label 'big_mem'
-
-  '''
-  <task script>
-  '''
-}
-```
-
-The same label can be applied to more than a process and multiple labels can be applied to the same process using the `label` directive more than one time.
-
-:::{note}
-A label must consist of alphanumeric characters or `_`, must start with an alphabetic character and must end with an alphanumeric character.
-:::
-
-Labels are useful to organise workflow processes in separate groups which can be referenced in the configuration file to select and configure subset of processes having similar computing requirements. See the {ref}`config-process-selectors` documentation for details.
-
-See also: [resourceLabels](#resourcelabels)
-
-(process-machinetype)=
-
-### machineType
-
-:::{versionadded} 19.07.0
-:::
-
-The `machineType` can be used to specify a predefined Google Compute Platform [machine type](https://cloud.google.com/compute/docs/machine-types) when running using the {ref}`Google Life Sciences <google-lifesciences-executor>` executor.
-
-This directive is optional and if specified overrides the cpus and memory directives:
-
-```groovy
-process foo {
-  machineType 'n1-highmem-8'
-
-  """
-  <your script here>
-  """
-}
-```
-
-See also: [cpus](#cpus) and [memory](#memory).
-
-(process-maxsubmitawait)=
-
-### maxSubmitAwait (experimental)
-
-The `maxSubmitAwait` directives allows you to specify how long a task can remain in submission queue without being executed.
-Elapsed this time the task execution will fail.
-
-When used along with `retry` error strategy, it can be useful to re-schedule the task to a difference queue or
-resource requirement. For example:
-
-```groovy
-process foo {
-  errorStrategy 'retry'
-  maxSubmitAwait '10 mins'
-  maxRetries 3
-  queue "${task.submitAttempt==1 : 'spot-compute' : 'on-demand-compute'}"
-  script:
-  '''
-  your_job --here
-  '''
-}
-```
-
-In the above example the task is submitted to the `spot-compute` on the first attempt (`task.submitAttempt==1`). If the
-task execution does not start in the 10 minutes, a failure is reported and a new submission is attempted using the
-queue named `on-demand-compute`.
-
-(process-maxerrors)=
-
-### maxErrors
-
-The `maxErrors` directive allows you to specify the maximum number of times a process can fail when using the `retry` error strategy. By default this directive is disabled, you can set it as shown in the example below:
-
-```groovy
-process retryIfFail {
-  errorStrategy 'retry'
-  maxErrors 5
-
-  """
-  echo 'do this as that .. '
-  """
-}
-```
-
-:::{note}
-This setting considers the **total** errors accumulated for a given process, across all instances. If you want to control the number of times a process **instance** (aka task) can fail, use `maxRetries`.
-:::
-
-See also: [errorStrategy](#errorstrategy) and [maxRetries](#maxretries).
-
-(process-maxforks)=
-
-### maxForks
-
-The `maxForks` directive allows you to define the maximum number of process instances that can be executed in parallel. By default this value is equals to the number of CPU cores available minus 1.
-
-If you want to execute a process in a sequential manner, set this directive to one. For example:
-
-```groovy
-process doNotParallelizeIt {
-  maxForks 1
-
-  '''
-  <your script here>
-  '''
-}
-```
-
-(process-maxretries)=
-
-### maxRetries
-
-The `maxRetries` directive allows you to define the maximum number of times a process instance can be re-submitted in case of failure. This value is applied only when using the `retry` error strategy. By default only one retry is allowed, you can increase this value as shown below:
-
-```groovy
-process retryIfFail {
-    errorStrategy 'retry'
-    maxRetries 3
-
-    """
-    echo 'do this as that .. '
-    """
-}
-```
-
-:::{note}
-There is a subtle but important difference between `maxRetries` and the `maxErrors` directive. The latter defines the total number of errors that are allowed during the process execution (the same process can launch different execution instances), while the `maxRetries` defines the maximum number of times the same process execution can be retried in case of an error.
-:::
-
-See also: [errorStrategy](#errorstrategy) and [maxErrors](#maxerrors).
-
-(process-memory)=
-
-### memory
-
-The `memory` directive allows you to define how much memory the process is allowed to use. For example:
-
-```groovy
-process big_job {
-    memory '2 GB'
-    executor 'sge'
-
-    """
-    your task script here
-    """
-}
-```
-
-The following memory unit suffix can be used when specifying the memory value:
-
-| Unit | Description |
-| ---- | ----------- |
-| B    | Bytes       |
-| KB   | Kilobytes   |
-| MB   | Megabytes   |
-| GB   | Gigabytes   |
-| TB   | Terabytes   |
-
-See {ref}`implicit-classes-memoryunit` for more information.
-
-See also: [cpus](#cpus), [time](#time), [queue](#queue) and [Dynamic computing resources](#dynamic-computing-resources).
-
-(process-module)=
-
-### module
-
-[Environment Modules](http://modules.sourceforge.net/) is a package manager that allows you to dynamically configure your execution environment and easily switch between multiple versions of the same software tool.
-
-If it is available in your system you can use it with Nextflow in order to configure the processes execution environment in your pipeline.
-
-In a process definition you can use the `module` directive to load a specific module version to be used in the process execution environment. For example:
-
-```groovy
-process basicExample {
-  module 'ncbi-blast/2.2.27'
-
-  """
-  blastp -query <etc..>
-  """
-}
-```
-
-You can repeat the `module` directive for each module you need to load. Alternatively multiple modules can be specified in a single `module` directive by separating all the module names by using a `:` (colon) character as shown below:
-
-```groovy
- process manyModules {
-
-   module 'ncbi-blast/2.2.27:t_coffee/10.0:clustalw/2.1'
-
-   """
-   blastp -query <etc..>
-   """
-}
-```
-
-(process-penv)=
-
-### penv
-
-The `penv` directive allows you to define the parallel environment to be used when submitting a parallel task to the {ref}`SGE <sge-executor>` resource manager. For example:
-
-```groovy
-process big_job {
-  cpus 4
-  penv 'smp'
-  executor 'sge'
-
-  """
-  blastp -query input_sequence -num_threads ${task.cpus}
-  """
-}
-```
-
-This configuration depends on the parallel environment provided by your grid engine installation. Refer to your cluster documentation or contact your admin to learn more about this.
-
-See also: [cpus](#cpus), [memory](#memory), [time](#time)
-
-(process-pod)=
-
-### pod
-
-The `pod` directive allows the definition of pod specific settings, such as environment variables, secrets, and config maps, when using the {ref}`k8s-executor` executor.
-
-For example:
-
-```groovy
-process your_task {
-  pod env: 'FOO', value: 'bar'
-
-  '''
-  echo $FOO
-  '''
-}
-```
-
-The above snippet defines an environment variable named `FOO` whose value is `bar`.
-
-When defined in the Nextflow configuration file, a pod setting can be defined as a map:
-
-```groovy
-process {
-  pod = [env: 'FOO', value: 'bar']
-}
-```
-
-Or as a list of maps:
-
-```groovy
-process {
-  pod = [
-    [env: 'FOO', value: 'bar'],
-    [secret: 'my-secret/key1', mountPath: '/etc/file.txt']
-  ]
-}
-```
-
-The following options are available:
-
-`affinity: <config>`
-: :::{versionadded} 22.01.0-edge
-  :::
-: Specifies the pod [affinity](https://kubernetes.io/docs/concepts/scheduling-eviction/assign-pod-node/#affinity-and-anti-affinity) with the given configuration.
-
-`annotation: '<name>', value: '<value>'`
-: *Can be specified multiple times*
-: Defines a pod [annotation](https://kubernetes.io/docs/concepts/overview/working-with-objects/annotations/) with the given name and value.
-
-`automountServiceAccountToken: true | false`
-: :::{versionadded} 22.01.0-edge
-  :::
-: Specifies whether to [automount service account token](https://kubernetes.io/docs/tasks/configure-pod-container/configure-service-account/#opt-out-of-api-credential-automounting) into the pod (default: `true`).
-
-`config: '<configMap>/<key>', mountPath: '</absolute/path>'`
-: *Can be specified multiple times*
-: Mounts a [ConfigMap](https://kubernetes.io/docs/tasks/configure-pod-container/configure-pod-configmap/) with name and optional key to the given path. If the key is omitted, the path is interpreted as a directory and all entries in the `ConfigMap` are exposed in that path.
-
-`csi: '<name>', mountPath: '</absolute/path>'`
-: :::{versionadded} 22.11.0-edge
-  :::
-: *Can be specified multiple times*
-: Mounts a [CSI ephemeral volume](https://kubernetes.io/docs/concepts/storage/ephemeral-volumes/#csi-ephemeral-volumes) by name to the given path.
-
-`emptyDir: <config>, mountPath: '</absolute/path>'`
-: :::{versionadded} 22.11.0-edge
-  :::
-: *Can be specified multiple times*
-: Mounts an [emptyDir](https://kubernetes.io/docs/concepts/storage/volumes/#emptydir) with the given configuration to the given path.
-
-`env: '<name>', config: '<configMap>/<key>'`
-: *Can be specified multiple times*
-: Defines an environment variable whose value is defined by the given [ConfigMap](https://kubernetes.io/docs/tasks/configure-pod-container/configure-pod-configmap/) and key.
-
-`env: '<name>', fieldPath: '<fieldPath>'`
-: :::{versionadded} 21.09.1-edge
-  :::
-: *Can be specified multiple times*
-: Defines an environment variable whose value is defined by the given [field path](https://kubernetes.io/docs/tasks/inject-data-application/environment-variable-expose-pod-information/#use-pod-fields-as-values-for-environment-variables) value.
-
-: For example, the following pod option:
-
-  ```groovy
-  pod = [env: 'MY_NODE_NAME', fieldPath: 'spec.nodeName']
-  ```
-
-  Maps to the following pod spec:
-
-  ```yaml
-  env:
-    - name: MY_NODE_NAME
-      valueFrom:
-        fieldRef:
-          fieldPath: spec.nodeName
-  ```
-
-`env: '<name>', secret: '<secret>/<key>'`
-: *Can be specified multiple times*
-: Defines an environment variable whose value is defined by the given [Secret](https://kubernetes.io/docs/concepts/configuration/secret/) and key.
-
-`env: '<name>', value: '<value>'`
-: *Can be specified multiple times*
-: Defines an environment variable with the given name and value.
-
-`hostPath: '/host/absolute/path', mountPath: '</pod/absolute/path>'`
-: :::{versionadded} 23.10.0
-  :::
-: *Can be specified multiple times*
-: Allows creating [hostPath](https://kubernetes.io/docs/concepts/storage/volumes/#hostpath) volume and access it with the specified `mountPath` in the pod.
-
-`imagePullPolicy: 'IfNotPresent' | 'Always' | 'Never'`
-: Specifies the [image pull policy](https://kubernetes.io/docs/concepts/containers/images/#image-pull-policy) used by the pod to pull the container image.
-
-`imagePullSecret: '<name>'`
-: Specifies the [image pull secret](https://kubernetes.io/docs/concepts/containers/images/#specifying-imagepullsecrets-on-a-pod) used to access a private container image registry.
-
-`label: '<name>', value: '<value>'`
-: *Can be specified multiple times*
-: Defines a pod [label](https://kubernetes.io/docs/concepts/overview/working-with-objects/labels/) with the given name and value.
-
-`nodeSelector: <config>`
-: Specifies the [node selector](https://kubernetes.io/docs/concepts/scheduling-eviction/assign-pod-node/#nodeselector) with the given configuration.
-
-: The configuration can be a map or a string:
-
-  ```groovy
-  // map
-  pod = [nodeSelector: [disktype: 'ssd', cpu: 'intel']]
-
-  // string
-  pod = [nodeSelector: 'disktype=ssd,cpu=intel']
-  ```
-
-`priorityClassName: '<name>'`
-: :::{versionadded} 22.01.0-edge
-  :::
-: Specifies the [priority class name](https://kubernetes.io/docs/concepts/scheduling-eviction/pod-priority-preemption/) for pods.
-
-`privileged: true | false`
-: :::{versionadded} 22.05.0-edge
-  :::
-: Specifies whether the pod should run as a *privileged* container (default: `false`).
-
-`runAsUser: '<uid>'`
-: Specifies the user ID with which to run the container. Shortcut for the `securityContext` option.
-
-`schedulerName: '<name>'`
-: Specifies which [scheduler](https://kubernetes.io/docs/tasks/extend-kubernetes/configure-multiple-schedulers/#specify-schedulers-for-pods) is used to schedule the container.
-
-`secret: '<secret>/<key>', mountPath: '</absolute/path>'`
-: *Can be specified multiple times*
-: Mounts a [Secret](https://kubernetes.io/docs/concepts/configuration/secret/) with name and optional key to the given path. If the key is omitted, the path is interpreted as a directory and all entries in the `Secret` are exposed in that path.
-
-`securityContext: <config>`
-: Specifies the pod [security context](https://kubernetes.io/docs/tasks/configure-pod-container/security-context/) with the given configuration.
-
-`toleration: <config>`
-: :::{versionadded} 22.04.0
-  :::
-: *Can be specified multiple times*
-: Specifies the pod [toleration](https://kubernetes.io/docs/concepts/scheduling-eviction/taint-and-toleration/) with the given configuration.
-
-: The configuration should be a map corresponding to a single toleration rule. For example, the following pod options:
-
-  ```groovy
-  pod = [
-      [toleration: [key: 'key1', operator: 'Equal', value: 'value1', effect: 'NoSchedule']],
-      [toleration: [key: 'key1', operator: 'Exists', effect: 'NoSchedule']],
-  ]
-  ```
-
-  Maps to the following pod spec:
-
-  ```yaml
-  tolerations:
-    - key: "key1"
-      operator: "Equal"
-      value: "value1"
-      effect: "NoSchedule"
-    - key: "key1"
-      operator: "Exists"
-      effect: "NoSchedule"
-  ```
-
-`ttlSecondsAfterFinished`
-: :::{versionadded} 24.02.0-edge
-  :::
-: Specifies the [TTL mechanism](https://kubernetes.io/docs/concepts/workloads/controllers/job/#ttl-mechanism-for-finished-jobs) for finished jobs in seconds. Applies to both successful and failed jobs.
-
-`volumeClaim: '<name>', mountPath: '</absolute/path>' [, subPath: '<path>', readOnly: true | false]`
-: *Can be specified multiple times*
-: Mounts a [Persistent volume claim](https://kubernetes.io/docs/concepts/storage/persistent-volumes/) with the given name to the given path.
-: The `subPath` option can be used to mount a sub-directory of the volume instead of its root.
-: The `readOnly` option can be used to mount the volume as read-only (default: `false`)
-
-(process-publishdir)=
-
-### publishDir
-
-The `publishDir` directive allows you to publish the process output files to a specified folder. For example:
-
-```groovy
-process foo {
-    publishDir '/data/chunks'
-
-    output:
-    path 'chunk_*'
-
-    '''
-    printf 'Hola' | split -b 1 - chunk_
-    '''
-}
-```
-
-The above example splits the string `Hola` into file chunks of a single byte. When complete the `chunk_*` output files are published into the `/data/chunks` folder.
-
-:::{note}
-Only files that match the declaration in the `output` block are published, not all the outputs of the process.
-:::
-
-:::{tip}
-The `publishDir` directive can be specified more than once in order to publish output files to different target directories based on different rules.
-:::
-
-By default files are published to the target folder creating a *symbolic link* for each process output that links the file produced into the process working directory. This behavior can be modified using the `mode` option, for example:
-
-```groovy
-process foo {
-    publishDir '/data/chunks', mode: 'copy', overwrite: false
-
-    output:
-    path 'chunk_*'
-
-    '''
-    printf 'Hola' | split -b 1 - chunk_
-    '''
-}
-```
-
-:::{warning}
-Files are copied into the specified directory in an *asynchronous* manner, so they may not be immediately available in the publish directory at the end of the process execution. For this reason, downstream processes should not try to access output files through the publish directory, but through channels.
-:::
-
-Available options:
-
-`contentType`
-: :::{versionadded} 22.10.0
-  :::
-: *Experimental: currently only supported for S3.*
-: Allow specifying the media content type of the published file a.k.a. [MIME type](https://developer.mozilla.org/en-US/docs/Web/HTTP/Basics_of_HTTP/MIME_Types). If set to `true`, the content type is inferred from the file extension (default: `false`).
-
-`enabled`
-: Enable or disable the publish rule depending on the boolean value specified (default: `true`).
-
-`failOnError`
-: :::{versionchanged} 24.03.0-edge
-  The default value was change from `false` to `true`
-  :::
-: When `true` abort the execution if some file can't be published to the specified target directory or bucket for any cause (default: `true`)
-
-`mode`
-: The file publishing method. Can be one of the following values:
-
-  - `'copy'`: Copies the output files into the publish directory.
-  - `'copyNoFollow'`: Copies the output files into the publish directory without following symlinks ie. copies the links themselves.
-  - `'link'`: Creates a hard link in the publish directory for each output file.
-  - `'move'`: Moves the output files into the publish directory. **Note**: this is only supposed to be used for a *terminal* process i.e. a process whose output is not consumed by any other downstream process.
-  - `'rellink'`: Creates a relative symbolic link in the publish directory for each output file.
-  - `'symlink'`: Creates an absolute symbolic link in the publish directory for each output file (default).
-
-`overwrite`
-: When `true` any existing file in the specified folder will be overridden (default: `true` during normal pipeline execution and `false` when pipeline execution is `resumed`).
-
-`path`
-: Specifies the directory where files need to be published. **Note**: the syntax `publishDir '/some/dir'` is a shortcut for `publishDir path: '/some/dir'`.
-
-`pattern`
-: Specifies a [glob][glob] file pattern that selects which files to publish from the overall set of output files.
-
-`saveAs`
-: A closure which, given the name of the file being published, returns the actual file name or a full path where the file is required to be stored. This can be used to rename or change the destination directory of the published files dynamically by using a custom strategy. Return the value `null` from the closure to *not* publish a file. This is useful when the process has multiple output files, but you want to publish only some of them.
-
-`storageClass`
-: :::{versionadded} 22.12.0-edge
-  :::
-: *Experimental: currently only supported for S3.*
-: Allow specifying the storage class to be used for the published file.
-
-`tags`
-: :::{versionadded} 21.12.0-edge
-  :::
-: *Experimental: currently only supported for S3.*
-: Allow the association of arbitrary tags with the published file e.g. `tags: [FOO: 'Hello world']`.
-
-(process-queue)=
-
-### queue
-
-The `queue` directive allows you to set the `queue` where jobs are scheduled when using a grid based executor in your pipeline. For example:
-
-```groovy
-process grid_job {
-    queue 'long'
-    executor 'sge'
-
-    """
-    your task script here
-    """
-}
-```
-
-:::{tip}
-Grid executors allow specifying multiple queue names separating them with a comma e.g. `queue 'short,long,cn-el6'`.
-However, this does not generally apply to other executors such as AWS Batch, Azure Batch, Google Batch.
-:::
-
-:::{note}
-This directive is only used by certain executors. Refer to the {ref}`executor-page` page to see which executors support this directive.
-:::
-
-(process-resourcelabels)=
-
-### resourceLabels
-
-:::{versionadded} 22.09.1-edge
-:::
-
-The `resourceLabels` directive allows you to specify custom name-value pairs that Nextflow applies to the computing resource used to carry out the process execution. Resource labels can be specified using the syntax shown below:
-
-```groovy
-process my_task {
-    resourceLabels region: 'some-region', user: 'some-username'
-
-    '''
-    <task script>
-    '''
-}
-```
-
-The limits and the syntax of the corresponding cloud provider should be taken into consideration when using resource labels.
-
-Resource labels are currently supported by the following executors:
-
-- {ref}`awsbatch-executor`
-- {ref}`azurebatch-executor`
-- {ref}`google-batch-executor`
-- {ref}`google-lifesciences-executor`
-- {ref}`k8s-executor`
-
-:::{versionadded} 23.09.0-edge
-Resource labels are supported for Azure Batch when using automatic pool creation.
-
-Resource labels in Azure are added to pools, rather than jobs, in order to facilitate cost analysis. A new pool will be created for each new set of resource labels, therefore it is recommended to also set `azure.batch.deletePoolsOnCompletion = true` when using process-specific resource labels.
-:::
-
-See also: [label](#label)
-
-(process-resourcelimits)=
-
-### resourceLimits
-
-:::{versionadded} 24.04.0
-:::
-
-The `resourceLimits` directive allows you to specify environment-specific limits for task resource requests. Resource limits can be specified in a process as follows:
-
-```groovy
-process my_task {
-  resourceLimits cpus: 24, memory: 768.GB, time: 72.h
-
-  script:
-  '''
-  your_command --here
-  '''
-}
-```
-
-Or in the Nextflow configuration:
-
-```groovy
-process {
-    resourceLimits = [ cpus: 24, memory: 768.GB, time: 72.h ]
-}
-```
-
-Resource limits can be defined for the following directives:
-
-- [cpus](#cpus)
-- [disk](#disk)
-- [memory](#memory)
-- [time](#time)
-
-Resource limits are a useful way to specify environment-specific limits alongside tasks with [dynamic resources](#dynamic-computing-resources). Normally, if a task requests more resources than can be provisioned (e.g. a task requests 32 cores but the largest node in the cluster has 24), the task will either fail or cause the pipeline to hang forever as it will never be scheduled. If the `resourceLimits` directive is defined with these limits, the task resources will be automatically reduced to comply with these limits before the job is submitted.
-
-(process-scratch)=
-
-### scratch
-
-The `scratch` directive allows you to execute the process in a temporary folder that is local to the execution node.
-
-This is useful when your pipeline is launched by using a grid executor, because it allows you to decrease the NFS overhead by running the pipeline processes in a temporary directory in the local disk of the actual execution node. Only the files declared as output in the process definition will be copied in the pipeline working area.
-
-In its basic form simply specify `true` at the directive value, as shown below:
-
-```groovy
-process simpleTask {
-  scratch true
-
-  output:
-  path 'data_out'
-
-  '''
-  <task script>
-  '''
-}
-```
-
-By doing this, it tries to execute the script in the directory defined by the variable `$TMPDIR` in the execution node. If this variable does not exist, it will create a new temporary directory by using the Linux command `mktemp`.
-
-:::{note}
-Cloud-based executors use `scratch = true` by default, since the work directory resides in object storage.
-:::
-
-The following values are supported:
-
-`false`
-: Do not use a scratch directory.
-
-`true`
-: Create a scratch directory in the directory defined by the `$TMPDIR` environment variable, or `$(mktemp /tmp)` if `$TMPDIR` is not set.
-
-`'$YOUR_VAR'`
-: Create a scratch directory in the directory defined by the given environment variable, or `$(mktemp /tmp)` if that variable is not set. The value must use single quotes, otherwise the environment variable will be evaluated in the pipeline script context.
-
-`'/my/tmp/path'`
-: Create a scratch directory in the specified directory.
-
-`'ram-disk'`
-: Create a scratch directory in the RAM disk `/dev/shm/`.
-
-(process-directive-shell)=
-
-### shell
-
-The `shell` directive allows you to define a custom shell command for process scripts. By default, script blocks are executed with `/bin/bash -ue`.
-
-```groovy
-process doMoreThings {
-    shell '/bin/bash', '-euo', 'pipefail'
-
-    '''
-    your_command_here
-    '''
-}
-```
-
-The same directive could be specified in your Nextflow configuration as follows:
-
-```groovy
-process.shell = ['/bin/bash', '-euo', 'pipefail']
-```
-
-(process-spack)=
-
-### spack
-
-The `spack` directive allows for the definition of the process dependencies using the [Spack](https://spack.io) package manager.
-
-Nextflow automatically sets up an environment for the given package names listed by in the `spack` directive. For example:
-
-```groovy
-process foo {
-    spack 'bwa@0.7.15'
-
-    '''
-    your_command --here
-    '''
-}
-```
-
-Multiple packages can be specified separating them with a blank space, e.g. `bwa@0.7.15 fastqc@0.11.5`.
-
-The `spack` directive also allows the specification of a Spack environment file path or the path of an existing environment directory. See the {ref}`spack-page` page for further details.
-
-(process-stageinmode)=
-
-### stageInMode
-
-The `stageInMode` directive defines how input files are staged into the process work directory. The following values are allowed:
-
-`'copy'`
-: Input files are staged in the process work directory by creating a copy.
-
-`'link'`
-: Input files are staged in the process work directory by creating a hard link for each of them.
-
-`'rellink'`
-: Input files are staged in the process work directory by creating a symbolic link with a relative path for each of them.
-
-`'symlink'`
-: Input files are staged in the process work directory by creating a symbolic link with an absolute path for each of them (default).
-
-(process-stageoutmode)=
-
-### stageOutMode
-
-The `stageOutMode` directive defines how output files are staged out from the scratch directory to the process work directory. The following values are allowed:
-
-`'copy'`
-: Output files are copied from the scratch directory to the work directory.
-
-`'fcp'`
-: :::{versionadded} 23.02.0-edge
-  :::
-: Output files are copied from the scratch directory to the work directory by using the [fcp](https://github.com/Svetlitski/fcp) utility (note: it must be available in your cluster computing nodes).
-
-`'move'`
-: Output files are moved from the scratch directory to the work directory.
-
-`'rclone'`
-: :::{versionadded} 23.01.0-edge
-  :::
-: Output files are copied from the scratch directory to the work directory by using the [rclone](https://rclone.org) utility (note: it must be available in your cluster computing nodes).
-
-`'rsync'`
-: Output files are copied from the scratch directory to the work directory by using the `rsync` utility.
-
-See also: [scratch](#scratch).
-
-(process-storedir)=
-
-### storeDir
-
-The `storeDir` directive allows you to define a directory that is used as a *permanent* cache for your process results.
-
-In more detail, it affects the process execution in two main ways:
-
-1. The process is executed only if the files declared in the `output` block do not exist in the directory specified by the `storeDir` directive. When the files exist the process execution is skipped and these files are used as the actual process result.
-2. Whenever a process is successfully completed the files listed in the `output` block are moved into the directory specified by the `storeDir` directive.
-
-The following example shows how to use the `storeDir` directive to create a directory containing a BLAST database for each species specified by an input parameter:
-
-```groovy
-process formatBlastDatabases {
-  storeDir '/db/genomes'
-
-  input:
-  path species
-
-  output:
-  path "${dbName}.*"
-
-  script:
-  dbName = species.baseName
-  """
-  makeblastdb -dbtype nucl -in ${species} -out ${dbName}
-  """
-}
-```
-
-:::{warning}
-The `storeDir` directive is meant for long-term process caching and should not be used to publish output files or organize outputs into a semantic directory structure. In those cases, use the [publishDir](#publishdir) directive instead.
-:::
-
-:::{note}
-The use of AWS S3 paths is supported, however it requires the installation of the [AWS CLI](https://aws.amazon.com/cli/) (i.e. `aws`) in the target compute node.
-:::
-
-(process-tag)=
-
-### tag
-
-The `tag` directive allows you to associate each process execution with a custom label, so that it will be easier to identify them in the log file or in the trace execution report. For example:
-
-```groovy
-process foo {
-  tag "$code"
-
-  input:
-  val code
-
-  """
-  echo $code
-  """
-}
-
-workflow {
-  Channel.of('alpha', 'gamma', 'omega') | foo
-}
-```
-
-The above snippet will print a log similar to the following one, where process names contain the tag value:
-
-```
-[6e/28919b] Submitted process > foo (alpha)
-[d2/1c6175] Submitted process > foo (gamma)
-[1c/3ef220] Submitted process > foo (omega)
-```
-
-See also {ref}`Trace execution report <trace-report>`
-
-(process-time)=
-
-### time
-
-The `time` directive allows you to define how long a process is allowed to run. For example:
-
-```groovy
-process big_job {
-    time '1h'
-
-    """
-    your task script here
-    """
-}
-```
-
-The following time unit suffixes can be used when specifying the duration value:
-
-| Unit                            | Description  |
-| ------------------------------- | ------------ |
-| `ms`, `milli`, `millis`         | Milliseconds |
-| `s`, `sec`, `second`, `seconds` | Seconds      |
-| `m`, `min`, `minute`, `minutes` | Minutes      |
-| `h`, `hour`, `hours`            | Hours        |
-| `d`, `day`, `days`              | Days         |
-
-Multiple units can be used in a single declaration, for example: `'1day 6hours 3minutes 30seconds'`
-
-See {ref}`implicit-classes-duration` for more information.
-
-:::{note}
-This directive is only used by certain executors. Refer to the {ref}`executor-page` page to see which executors support this directive.
-:::
-
-See also: [cpus](#cpus), [memory](#memory), [queue](#queue) and [Dynamic computing resources](#dynamic-computing-resources).
-
-### Dynamic directives
-
-A directive can be assigned *dynamically*, during the process execution, so that its actual value can be evaluated based on the process inputs.
-
-In order to be defined in a dynamic manner, the directive's value needs to be expressed using a {ref}`closure <script-closure>`, as in the following example:
-
-```groovy
-process foo {
-  executor 'sge'
-  queue { entries > 100 ? 'long' : 'short' }
-
-  input:
-  tuple val(entries), path('data.txt')
-
-  script:
-  """
-  < your job here >
-  """
-}
-```
-
-In the above example, the [queue](#queue) directive is evaluated dynamically, depending on the input value `entries`. When it is larger than 100, jobs will be submitted to the `long` queue, otherwise the `short` queue will be used.
-
-All directives can be assigned a dynamic value except the following:
-
-- [executor](#executor)
-- [label](#label)
-- [maxForks](#maxforks)
-
-:::{tip}
-Assigning a string value with one or more variables is always resolved in a dynamic manner, and therefore is equivalent to the above syntax. For example, the above directive can also be written as:
-
-```groovy
-queue "${ entries > 100 ? 'long' : 'short' }"
-```
-
-Note, however, that the latter syntax can be used both for a directive's main argument (as in the above example) and for a directive's optional named attributes, whereas the closure syntax is only resolved dynamically for a directive's main argument.
-:::
-
-:::{tip}
-You can retrieve the current value of a dynamic directive in the process script by using the implicit variable `task`, which holds the directive values defined in the current task. For example:
-
-```groovy
-process foo {
-  queue { entries > 100 ? 'long' : 'short' }
-
-  input:
-  tuple val(entries), path('data.txt')
-
-  script:
   """
-  echo Current queue: ${task.queue}
-  """
-}
-```
-:::
-
-### Dynamic computing resources
-
-It's a very common scenario that different instances of the same process may have very different needs in terms of computing resources. In such situations requesting, for example, an amount of memory too low will cause some tasks to fail. Instead, using a higher limit that fits all the tasks in your execution could significantly decrease the execution priority of your jobs.
-
-The [Dynamic directives](#dynamic-directives) evaluation feature can be used to modify the amount of computing resources requested in case of a process failure and try to re-execute it using a higher limit. For example:
-
-```groovy
-process foo {
-    memory { 2.GB * task.attempt }
-    time { 1.hour * task.attempt }
-
-    errorStrategy { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
-    maxRetries 3
-
-    script:
-    <your job here>
-}
-```
-
-In the above example the [memory](#memory) and execution [time](#time) limits are defined dynamically. The first time the process is executed the `task.attempt` is set to `1`, thus it will request a two GB of memory and one hour of maximum execution time.
-
-If the task execution fail reporting an exit status in the range between 137 and 140, the task is re-submitted (otherwise terminates immediately). This time the value of `task.attempt` is `2`, thus increasing the amount of the memory to four GB and the time to 2 hours, and so on.
-
-The directive [maxRetries](#maxretries) set the maximum number of time the same task can be re-executed.
-
-### Dynamic Retry with backoff
-
-There are cases in which the required execution resources may be temporary unavailable e.g. network congestion. In these cases immediately re-executing the task will likely result in the identical error. A retry with an exponential backoff delay can better recover these error conditions:
-
-```groovy
-process foo {
-  errorStrategy { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
-  maxRetries 5
-
-  script:
-  '''
-  your_command --here
-  '''
 }
 ```
 
diff --git a/docs/reference/channel.md b/docs/reference/channel.md
new file mode 100644
index 0000000000..13e2bfd414
--- /dev/null
+++ b/docs/reference/channel.md
@@ -0,0 +1,513 @@
+(channel-factory)=
+
+# Channel factories
+
+(channel-empty)=
+
+## empty
+
+The `channel.empty` factory method, by definition, creates a channel that doesn't emit any value.
+
+See also: {ref}`operator-ifempty`.
+
+(channel-from)=
+
+## from
+
+:::{deprecated} 19.09.0-edge
+Use [channel.of](#of) or [channel.fromList](#fromlist) instead.
+:::
+
+The `channel.from` method allows you to create a channel emitting any sequence of values that are specified as the method argument, for example:
+
+```nextflow
+ch = channel.from( 1, 3, 5, 7 )
+ch.subscribe { v -> println "value: $v" }
+```
+
+The first line in this example creates a variable `ch` which holds a channel object. This channel emits the values specified as a parameter in the `from` method. Thus the second line will print the following:
+
+```
+value: 1
+value: 3
+value: 5
+value: 7
+```
+
+The following example shows how to create a channel from a *range* of numbers or strings:
+
+```nextflow
+zeroToNine = channel.from( 0..9 )
+strings = channel.from( 'A'..'Z' )
+```
+
+:::{note}
+When the `channel.from` argument is an object implementing the (Java) [Collection](http://docs.oracle.com/javase/7/docs/api/java/util/Collection.html) interface, the resulting channel emits the collection entries as individual items.
+:::
+
+Thus the following two declarations produce an identical result even though in the first case the items are specified as multiple arguments while in the second case as a single list object argument:
+
+```nextflow
+channel.from( 1, 3, 5, 7, 9 )
+channel.from( [1, 3, 5, 7, 9] )
+```
+
+But when more than one argument is provided, they are always managed as *single* emissions. Thus, the following example creates a channel emitting three entries each of which is a list containing two elements:
+
+```nextflow
+channel.from( [1, 2], [5,6], [7,9] )
+```
+
+(channel-fromlist)=
+
+## fromList
+
+:::{versionadded} 19.10.0
+:::
+
+The `channel.fromList` method allows you to create a channel emitting the values provided as a list of elements, for example:
+
+```nextflow
+channel
+    .fromList( ['a', 'b', 'c', 'd'] )
+    .view { v -> "value: $v" }
+```
+
+Prints:
+
+```
+value: a
+value: b
+value: c
+value: d
+```
+
+See also: [channel.of](#of) factory method.
+
+(channel-path)=
+
+## fromPath
+
+You can create a channel emitting one or more file paths by using the `channel.fromPath` method and specifying a path
+string as an argument. For example:
+
+```nextflow
+myFileChannel = channel.fromPath( '/data/some/bigfile.txt' )
+```
+
+The above line creates a channel and binds it to a [Path](http://docs.oracle.com/javase/7/docs/api/java/nio/file/Path.html)
+object for the specified file.
+
+:::{note}
+`channel.fromPath` does not check whether the file exists.
+:::
+
+Whenever the `channel.fromPath` argument contains a `*` or `?` wildcard character it is interpreted as a [glob][glob] path matcher.
+For example:
+
+```nextflow
+myFileChannel = channel.fromPath( '/data/big/*.txt' )
+```
+
+This example creates a channel and emits as many `Path` items as there are files with `txt` extension in the `/data/big` folder.
+
+:::{tip}
+Two asterisks, i.e. `**`, works like `*` but crosses directory boundaries. This syntax is generally used for matching complete paths. Curly brackets specify a collection of sub-patterns.
+:::
+
+For example:
+
+```nextflow
+files = channel.fromPath( 'data/**.fa' )
+moreFiles = channel.fromPath( 'data/**/*.fa' )
+pairFiles = channel.fromPath( 'data/file_{1,2}.fq' )
+```
+
+The first line returns a channel emitting the files ending with the suffix `.fa` in the `data` folder *and* recursively in all its sub-folders. While the second one only emits the files which have the same suffix in *any* sub-folder in the `data` path. Finally the last example emits two files: `data/file_1.fq` and `data/file_2.fq`.
+
+:::{note}
+As in Linux Bash, the `*` wildcard does not catch hidden files (i.e. files whose name starts with a `.` character).
+:::
+
+Multiple paths or glob patterns can be specified using a list:
+
+```nextflow
+channel.fromPath( ['/some/path/*.fq', '/other/path/*.fastq'] )
+```
+
+In order to include hidden files, you need to start your pattern with a period character or specify the `hidden: true` option. For example:
+
+```nextflow
+expl1 = channel.fromPath( '/path/.*' )
+expl2 = channel.fromPath( '/path/.*.fa' )
+expl3 = channel.fromPath( '/path/*', hidden: true )
+```
+
+The first example returns all hidden files in the specified path. The second one returns all hidden files ending with the `.fa` suffix. Finally the last example returns all files (hidden and non-hidden) in that path.
+
+By default a [glob][glob] pattern only looks for regular file paths that match the specified criteria, i.e. it won't return directory paths.
+
+You can use the `type` option specifying the value `file`, `dir` or `any` in order to define what kind of paths you want. For example:
+
+```nextflow
+myFileChannel = channel.fromPath( '/path/*b', type: 'dir' )
+myFileChannel = channel.fromPath( '/path/a*', type: 'any' )
+```
+
+The first example will return all *directory* paths ending with the `b` suffix, while the second will return any file or directory starting with a `a` prefix.
+
+Available options:
+
+`checkIfExists`
+: When `true` throws an exception of the specified path do not exist in the file system (default: `false`)
+
+`followLinks`
+: When `true` it follows symbolic links during directories tree traversal, otherwise they are managed as files (default: `true`)
+
+`glob`
+: When `true` interprets characters `*`, `?`, `[]` and `{}` as glob wildcards, otherwise handles them as normal characters (default: `true`)
+
+`hidden`
+: When `true` includes hidden files in the resulting paths (default: `false`)
+
+`maxDepth`
+: Maximum number of directory levels to visit (default: no limit)
+
+`relative`
+: When `true` returned paths are relative to the top-most common directory (default: `false`)
+
+`type`
+: Type of paths returned, either `file`, `dir` or `any` (default: `file`)
+
+(channel-filepairs)=
+
+## fromFilePairs
+
+The `channel.fromFilePairs` method creates a channel emitting the file pairs matching a [glob][glob] pattern provided
+by the user. The matching files are emitted as tuples in which the first element is the grouping key of the matching pair and the second element is the list of files (sorted in lexicographical order). For example:
+
+```nextflow
+channel
+    .fromFilePairs('/my/data/SRR*_{1,2}.fastq')
+    .view()
+```
+
+It will produce an output similar to the following:
+
+```
+[SRR493366, [/my/data/SRR493366_1.fastq, /my/data/SRR493366_2.fastq]]
+[SRR493367, [/my/data/SRR493367_1.fastq, /my/data/SRR493367_2.fastq]]
+[SRR493368, [/my/data/SRR493368_1.fastq, /my/data/SRR493368_2.fastq]]
+[SRR493369, [/my/data/SRR493369_1.fastq, /my/data/SRR493369_2.fastq]]
+[SRR493370, [/my/data/SRR493370_1.fastq, /my/data/SRR493370_2.fastq]]
+[SRR493371, [/my/data/SRR493371_1.fastq, /my/data/SRR493371_2.fastq]]
+```
+
+:::{note}
+The glob pattern must contain at least one `*` wildcard character.
+:::
+
+Multiple glob patterns can be specified using a list:
+
+```nextflow
+channel.fromFilePairs( ['/some/data/SRR*_{1,2}.fastq', '/other/data/QFF*_{1,2}.fastq'] )
+```
+
+Alternatively, it is possible to implement a custom file pair grouping strategy providing a closure which, given the current file as parameter, returns the grouping key. For example:
+
+```nextflow
+channel
+    .fromFilePairs('/some/data/*', size: -1) { file -> file.extension }
+    .view { ext, files -> "Files with the extension $ext are $files" }
+```
+
+Available options:
+
+`checkIfExists`
+: When `true` throws an exception of the specified path do not exist in the file system (default: `false`)
+
+`followLinks`
+: When `true` it follows symbolic links during directories tree traversal, otherwise they are managed as files (default: `true`)
+
+`flat`
+: When `true` the matching files are produced as sole elements in the emitted tuples (default: `false`).
+
+`hidden`
+: When `true` includes hidden files in the resulting paths (default: `false`)
+
+`maxDepth`
+: Maximum number of directory levels to visit (default: no limit)
+
+`size`
+: Defines the number of files each emitted item is expected to hold (default: 2). Set to `-1` for any.
+
+`type`
+: Type of paths returned, either `file`, `dir` or `any` (default: `file`)
+
+(channel-fromsra)=
+
+## fromSRA
+
+:::{versionadded} 19.04.0
+:::
+
+The `channel.fromSRA` method queries the [NCBI SRA](https://www.ncbi.nlm.nih.gov/sra) database and returns a channel emitting the FASTQ files matching the specified criteria i.e project or accession number(s). For example:
+
+```nextflow
+channel
+    .fromSRA('SRP043510')
+    .view()
+```
+
+It returns:
+
+```
+[SRR1448794, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/004/SRR1448794/SRR1448794.fastq.gz]
+[SRR1448795, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/005/SRR1448795/SRR1448795.fastq.gz]
+[SRR1448792, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/002/SRR1448792/SRR1448792.fastq.gz]
+[SRR1448793, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/003/SRR1448793/SRR1448793.fastq.gz]
+[SRR1910483, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/003/SRR1910483/SRR1910483.fastq.gz]
+[SRR1910482, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/002/SRR1910482/SRR1910482.fastq.gz]
+(remaining omitted)
+```
+
+Multiple accession IDs can be specified using a list object:
+
+```nextflow
+ids = ['ERR908507', 'ERR908506', 'ERR908505']
+channel
+    .fromSRA(ids)
+    .view()
+```
+
+```
+[ERR908507, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908507/ERR908507_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908507/ERR908507_2.fastq.gz]]
+[ERR908506, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908506/ERR908506_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908506/ERR908506_2.fastq.gz]]
+[ERR908505, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908505/ERR908505_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908505/ERR908505_2.fastq.gz]]
+```
+
+:::{note}
+Each read pair is implicitly managed and returned as a list of files.
+:::
+
+This method uses the NCBI [ESearch](https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch) API behind the scenes, therefore it allows the use of any query term supported by this API.
+
+To access the ESearch API, you must provide your [NCBI API keys](https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities) through one of the following ways:
+
+- The `apiKey` option:
+  ```nextflow
+  channel.fromSRA(ids, apiKey:'0123456789abcdef')
+  ```
+
+- The `NCBI_API_KEY` variable in your environment:
+  ```bash
+  export NCBI_API_KEY=0123456789abcdef
+  ```
+
+Available options:
+
+`apiKey`
+: NCBI user API key.
+
+`cache`
+: Enable/disable the caching API requests (default: `true`).
+
+`max`
+: Maximum number of entries that can be retried (default: unlimited) .
+
+`protocol`
+: Allow choosing the protocol for the resulting remote URLs. Available choices: `ftp`, `http`, `https` (default: `ftp`).
+
+`retryPolicy`
+: Set a retry policy in case the SRA request fails with a retriable error.
+The retry policy is set as a Map specifying the different policy properties.
+
+Available retry policy properties:
+
+| Property      | Description                                     | Default |
+| ------------- |-------------------------------------------------| ------- |
+| `delay`       | Delay when retrying failed SRA requests.        | `500ms` |
+| `jitter`      | Jitter value when retrying failed SRA requests. | `0.25`  |
+| `maxAttempts` | Max attempts when retrying failed SRA requests. | `3`     |
+| `maxDelay`    | Max delay when retrying failed SRA requests.    | `30s`   |
+
+The following code snippet shows an example for using the `Channel.fromSRA` factory method with a custom `retryPolicy`.
+
+  ```nextflow
+  channel.fromSRA(ids, retryPolicy: [delay: '250ms', maxAttempts: 5])
+  ```
+
+(channel-interval)=
+
+## interval
+
+The `interval` method emits an incrementing index (starting from zero) at a periodic interval. For example:
+
+```nextflow
+Channel.interval('1s').view()
+```
+
+The above snippet will emit 0, 1, 2, and so on, every second, forever. You can use an operator such as {ref}`operator-take` or {ref}`operator-until` to close the channel based on a stopping condition.
+
+An optional closure can be used to transform the index. Additionally, returning `Channel.STOP` will close the channel. For example:
+
+```nextflow
+ch = Channel.interval('1s') { i ->
+    i == 10 ? Channel.STOP : i
+}
+ch.view()
+```
+
+(channel-of)=
+
+## of
+
+:::{versionadded} 19.10.0
+:::
+
+The `channel.of` method allows you to create a channel that emits the arguments provided to it, for example:
+
+```nextflow
+ch = channel.of( 1, 3, 5, 7 )
+ch.view { v -> "value: $v" }
+```
+
+The first line in this example creates a variable `ch` which holds a channel object. This channel emits the arguments
+supplied to the `of` method. Thus the second line prints the following:
+
+```
+value: 1
+value: 3
+value: 5
+value: 7
+```
+
+Ranges of values are expanded accordingly:
+
+```nextflow
+channel
+    .of(1..23, 'X', 'Y')
+    .view()
+```
+
+Prints:
+
+```
+1
+2
+3
+4
+:
+23
+X
+Y
+```
+
+See also: [channel.fromList](#fromlist) factory method.
+
+(channel-topic)=
+
+## topic
+
+:::{versionadded} 23.11.0-edge
+:::
+
+:::{note}
+This feature requires the `nextflow.preview.topic` feature flag to be enabled.
+:::
+
+A *topic channel* is a queue channel that can receive values from many source channels *implicitly* based on a matching *topic name*.
+
+:::{tip}
+You can think of it as a channel that is shared across many different processes using the same topic name.
+:::
+
+A process output can be assigned to a topic using the `topic` option on an output, for example:
+
+```nextflow
+process foo {
+  output:
+  val('foo'), topic: my_topic
+
+  // ...
+}
+
+process bar {
+  output:
+  val('bar'), topic: my_topic
+
+  // ...
+}
+```
+
+The `channel.topic` method allows referencing the topic channel with the specified name, which can be used as a process
+input or operator composition as any other Nextflow channel:
+
+```nextflow
+channel.topic('my-topic').view()
+```
+
+This approach is a convenient way to collect related items from many different sources without explicitly connecting them (e.g. using the `mix` operator).
+
+:::{warning}
+Any process that consumes a topic channel (directly or indirectly) should not send any outputs to that topic, or else the pipeline will hang forever.
+:::
+
+See also: {ref}`process-additional-options` for process outputs.
+
+(channel-value)=
+
+## value
+
+The `channel.value` method is used to create a value channel. An optional (not `null`) argument can be specified to bind
+the channel to a specific value. For example:
+
+```nextflow
+expl1 = channel.value()
+expl2 = channel.value( 'Hello there' )
+expl3 = channel.value( [1,2,3,4,5] )
+```
+
+The first line in the example creates an 'empty' variable. The second line creates a channel and binds a string to it.
+The third line creates a channel and binds a list object to it that will be emitted as a single value.
+
+(channel-watchpath)=
+
+## watchPath
+
+The `channel.watchPath` method watches a folder for one or more files matching a specified pattern. As soon as there
+is a file that meets the specified condition, it is emitted over the channel that is returned by the `watchPath` method.
+The condition on files to watch can be specified by using `*` or `?` wildcard characters i.e. by specifying a [glob][glob] path matching criteria.
+
+For example:
+
+```nextflow
+channel
+    .watchPath( '/path/*.fa' )
+    .subscribe { fa -> println "Fasta file: $fa" }
+```
+
+By default it watches only for new files created in the specified folder. Optionally, it is possible to provide a second
+argument that specifies what event(s) to watch. The supported events are:
+
+- `create`: A new file is created (default)
+- `modify`: A file is modified
+- `delete`: A file is deleted
+
+You can specify more than one of these events by using a comma separated string as shown below:
+
+```nextflow
+channel
+    .watchPath( '/path/*.fa', 'create,modify' )
+    .subscribe { fa -> println "File created or modified: $fa" }
+```
+
+:::{warning}
+The `channel.watchPath` factory waits endlessly for files that match the specified pattern and event(s), which means
+that it will cause your pipeline to run forever. Consider using the `take` or `until` operator to close the channel when
+a certain condition is met (e.g. after receiving 10 files, receiving a file named `DONE`).
+:::
+
+See also: [channel.fromPath](#frompath) factory method.
+
+[glob]: http://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob
diff --git a/docs/reference/cli.md b/docs/reference/cli.md
new file mode 100644
index 0000000000..591d1fa151
--- /dev/null
+++ b/docs/reference/cli.md
@@ -0,0 +1,1298 @@
+(cli-reference)=
+
+# CLI reference
+
+This page lists all of the available options and subcommands for the {ref}`Nextflow CLI <cli-page>`.
+
+(cli-options)=
+
+## Options
+
+The top-level options are meant to be invoked in relation to the core Nextflow application and are applied to all commands. For options specific to any command, refer the CLI Commands section.
+
+Available options:
+
+`-C`
+: Use the specified configuration file(s) overriding any defaults.
+
+`-D`
+: Set JVM properties.
+
+`-bg`
+: Execute nextflow in background.
+
+`-c, -config`
+: Add the specified file to configuration set.
+
+`-d, -dockerize`
+: :::{deprecated} 23.09.0-edge
+  :::
+: Launch nextflow via Docker (experimental).
+
+`-h`
+: Print this help.
+
+`-log`
+: Set nextflow log file path.
+
+`-q, -quiet`
+: Do not print information messages.
+
+`-remote-debug`
+: Enable JVM interactive remote debugging (experimental).
+
+`-syslog`
+: Send logs to syslog server (e.g. localhost:514).
+
+`-trace`
+: Enable trace level logging for the specified packages. Multiple packages can be provided separating them with a comma, e.g. `-trace nextflow,io.seqera`.
+
+`-v, -version`
+: Print the program version.
+
+## Commands
+
+(cli-clean)=
+
+### `clean`
+
+Clean up *cache* and *work* directories.
+
+**Usage**
+
+```console
+$ nextflow clean [run_name|session_id] [options]
+```
+
+**Description**
+
+Upon invocation within a directory, `nextflow` creates a project specific `.nextflow.log` file, `.nextflow` cache directory as well as a `work` directory. The `clean` command is designed to facilitate removal of these files from previous executions. A list of run names and session ids can be generated by invoking `nextflow log -q`.
+
+If no run name or session id is provided, it will clean the latest run.
+
+**Options**
+
+`-after`
+: Clean up runs executed *after* the specified one.
+
+`-before`
+: Clean up runs executed *before* the specified one.
+
+`-but`
+: Clean up all runs *except* the specified one.
+
+`-n, -dry-run`
+: Print names of files to be removed without deleting them.
+
+`-f, -force`
+: Force clean command.
+
+`-h, -help`
+: Print the command usage.
+
+`-k, -keep-logs`
+: Removes only temporary files but retains execution log entries and metadata.
+
+`-q, -quiet`
+: Do not print names of files removed.
+
+**Examples**
+
+Dry run to remove work directories for the run name `boring_euler`:
+
+```console
+$ nextflow clean boring_euler -n
+
+Would remove work/92/c1a9cd9a96e0531d81ca69f5dc3bb7
+Would remove work/3f/70944c7a549b6221e1ccc7b4b21b62
+Would remove work/0e/2ebdba85f76f6068b21a1bcbf10cab
+```
+
+Remove work directories for the run name `boring_euler`.
+
+```console
+$ nextflow clean boring_euler -f
+
+Removed work/92/c1a9cd9a96e0531d81ca69f5dc3bb7
+Removed work/3f/70944c7a549b6221e1ccc7b4b21b62
+Removed work/0e/2ebdba85f76f6068b21a1bcbf10cab
+```
+
+Remove the execution entries *except* for a specific execution.
+
+```console
+$ nextflow clean -but tiny_leavitt -f
+
+Removed work/1f/f1ea9158fb23b53d5083953121d6b6
+Removed work/bf/334115deec60929dc18edf0010032a
+Removed work/a3/06521d75da296d4dd7f4f8caaddad8
+```
+
+Dry run to remove the execution data *before* a specific execution.
+
+```console
+$ nextflow clean -before tiny_leavitt -n
+
+Would remove work/5d/ad76f7b7ab3500cf616814ef644b61
+Would remove work/c4/69a82b080a477612ba8d8e4c27b579
+Would remove work/be/a4fa2aa38f76fd324958c81c2e4603
+Would remove work/54/39116773891c47a91e3c1733aad4de
+```
+
+Dry run to remove the execution data *after* a specific execution.
+
+```console
+$ nextflow clean -after focused_payne -n
+
+Would remove work/1f/f1ea9158fb23b53d5083953121d6b6
+Would remove work/bf/334115deec60929dc18edf0010032a
+Would remove work/a3/06521d75da296d4dd7f4f8caaddad8
+```
+
+Dry run to remove the temporary execution data for a specific execution, while keeping the log files.
+
+```console
+$ nextflow clean -keep-logs tiny_leavitt -n
+
+Would remove temp files from work/1f/f1ea9158fb23b53d5083953121d6b6
+Would remove temp files from work/bf/334115deec60929dc18edf0010032a
+Would remove temp files from work/a3/06521d75da296d4dd7f4f8caaddad8
+```
+
+### `clone`
+
+Clone a remote project into a folder.
+
+**Usage**
+
+```console
+$ nextflow clone [options] [project]
+```
+
+**Description**
+
+The `clone` command downloads a pipeline from a Git-hosting platform into the *current directory* and modifies it accordingly. For downloading a pipeline into the global cache `~/.nextflow/assets`, please refer to the `nextflow pull` command.
+
+**Options**
+
+`-d, -deep`
+: Create a shallow clone of the specified depth.
+
+`-h, -help`
+: Print the command usage.
+
+`-hub` (`github`)
+: Service hub where the project is hosted. Options: `gitlab` or `bitbucket`.
+
+`-r` (`master`)
+: Revision to clone - It can be a git branch, tag, or revision number.
+
+`-user`
+: Private repository user name.
+
+**Examples**
+
+Clone the latest revision of a pipeline.
+
+```console
+$ nextflow clone nextflow-io/hello
+nextflow-io/hello cloned to: hello
+```
+
+Clone a specific revision of a pipeline.
+
+```console
+$ nextflow clone nextflow-io/hello -r v1.1
+nextflow-io/hello cloned to: hello
+```
+
+### `config`
+
+Print the resolved pipeline configuration.
+
+**Usage**
+
+```console
+$ nextflow config [options] [project name or path]
+```
+
+**Description**
+
+The `config` command is used for printing the project's configuration i.e. the `nextflow.config` and is especially useful for understanding the resolved profiles and parameters that Nextflow will use run a pipeline. For in-depth information, please refer the {ref}`config-profiles` section.
+
+**Options**
+
+`-flat`
+: Print config using flat notation.
+
+`-h, -help`
+: Print the command usage.
+
+`-profile`
+: Choose a configuration profile.
+
+`-properties`
+: Print config using Java properties notation.
+
+`-a, -show-profiles`
+: Show all configuration profiles.
+
+`-sort`
+: Sort config attributes.
+
+`-value`
+: :::{versionadded} 23.08.0-edge
+  :::
+: Print the value of a config option, or fail if the option is not defined.
+
+**Examples**
+
+Print out the inferred config using a the default group key-value notation.
+
+```console
+$ nextflow config
+
+docker {
+    enabled = true
+}
+
+process {
+    executor = 'local'
+}
+```
+
+Print out the config using a flat notation.
+
+```console
+$ nextflow config -flat
+
+docker.enabled = true
+process.executor = 'local'
+```
+
+Print out the config using the Java properties notation.
+
+```console
+$ nextflow config -properties
+
+docker.enabled = true
+process.executor = local
+```
+
+Print out the value of a specific configuration property.
+
+```console
+$ nextflow config -value process.executor
+local
+```
+
+Print out all profiles from the project's configuration.
+
+```console
+$ nextflow config -show-profiles
+
+docker {
+    enabled = true
+}
+
+profiles {
+    standard {
+        process {
+            executor = 'local'
+        }
+    }
+    cloud {
+        process {
+            executor = 'cirrus'
+            container = 'cbcrg/imagex'
+        }
+    }
+}
+```
+
+(cli-console)=
+
+### `console`
+
+Launch the Nextflow interactive console.
+
+**Usage**
+
+```console
+$ nextflow console
+```
+
+**Description**
+
+The `console` command provides a Graphical User Interface (GUI) and an interactive REPL (Read-Eval-Print-Loop) for quick experimentation.
+
+**Options**
+
+None available
+
+**Examples**
+
+Launch the `console` GUI.
+
+```console
+$ nextflow console
+```
+
+### `drop`
+
+Delete the local copy of a project.
+
+**Usage**
+
+```console
+$ nextflow drop [options] [project]
+```
+
+**Description**
+
+The `drop` command is used to remove the projects which have been downloaded into the global cache. Please refer the `list` command for generating a list of downloaded pipelines.
+
+**Options**
+
+`-f`
+: Delete the repository without taking care of local changes.
+
+`-h, -help`
+: Print the command usage.
+
+**Examples**
+
+Drop the `nextflow-io/hello` project.
+
+```console
+$ nextflow drop nextflow-io/hello
+```
+
+Forcefully drop the `nextflow-io/hello` pipeline, ignoring any local changes.
+
+```console
+$ nextflow drop nextflow-io/hello -f
+```
+
+### `fs`
+
+Perform basic filesystem operations.
+
+**Usage**
+
+```console
+$ nextflow fs [subcommands]
+```
+
+**Description**
+
+The `fs` command is used to perform filesystem operations like copy, move, delete, list directory, etc. Like the `file()` method, it can work with local files, remote URLs, and remote object storage. Storage credentials can be provided through the same manner as launching a pipeline (Nextflow config, environment vars, etc).
+
+**Options**
+
+`-h, -help`
+: Print the command usage.
+
+**Examples**
+
+List a directory.
+
+```console
+$ nextflow fs list <directory>
+```
+
+Print the contents of a file to standard output.
+
+```console
+$ nextflow fs cat <file>
+```
+
+Copy a file or directory.
+
+```console
+$ nextflow fs cp <source> <target>
+```
+
+Move a file or directory.
+
+```console
+$ nextflow fs mv <source> <target>
+```
+
+Delete a file or directory.
+
+```console
+$ nextflow fs rm <path>
+```
+
+:::{versionadded} 23.10.0
+:::
+
+Print file or directory attributes.
+
+```console
+$ nextflow fs stat <path>
+```
+
+### `help`
+
+Print the top-level help or specific help for a command.
+
+**Usage**
+
+```console
+$ nextflow help [options] [command]
+```
+
+**Description**
+
+The `help` command prints out the overview of the CLI interface and enumerates the top-level *options* and *commands*. Note that this command is equivalent to simply invoking `nextflow` at the command line.
+
+**Options**
+
+`-h, -help`
+: Print the command usage.
+
+**Examples**
+
+Invoke the `help` option for the `drop` command.
+
+```console
+$ nextflow help drop
+
+Delete the local copy of a project
+Usage: drop [options] name of the project to drop
+   Options:
+     -f
+          Delete the repository without taking care of local changes
+          Default: false
+     -h, -help
+          Print the command usage
+          Default: false
+```
+
+### `info`
+
+Print project or system runtime information.
+
+**Usage**
+
+```console
+$ nextflow info [options] [project]
+```
+
+**Description**
+
+The `info` command prints out the nextflow runtime information about the hardware as well as the software versions of the Nextflow version and build, operating system, and Groovy and Java runtime. It can also be used to display information about a specific project.
+
+If no run name or session id is provided, it will clean the latest run.
+
+**Options**
+
+`-u, -check-updates`
+: Check for remote updates.
+
+`-d`
+: Show detailed information.
+
+`-h, -help`
+: Print the command usage.
+
+`-o` (`text`)
+: Output format, either `text`, `json` or `yaml`.
+
+**Examples**
+
+Display Nextflow runtime and system info:
+
+```console
+$ nextflow info
+
+  Version: 20.07.1 build 5412
+  Created: 24-07-2020 15:18 UTC (20:48 IDT)
+  System: Mac OS X 10.15.6
+  Runtime: Groovy 2.5.11 on OpenJDK 64-Bit Server VM 1.8.0_192-b01
+  Encoding: UTF-8 (UTF-8)
+```
+
+Display information about a specific project:
+
+```console
+$ nextflow info nextflow-io/hello
+
+  project name: nextflow-io/hello
+  repository  : https://github.com/nextflow-io/hello
+  local path  : /Users/evanfloden/.nextflow/assets/nextflow-io/hello
+  main script : main.nf
+  revisions   :
+  * master (default)
+    mybranch
+    testing
+    v1.1 [t]
+    v1.2 [t]
+```
+
+### `inspect`
+
+:::{versionadded} 23.09.0-edge
+:::
+
+Inspect process settings in a pipeline project. Currently only supports the `container` directive.
+
+**Usage**
+
+```console
+$ nextflow inspect [options] [project]
+```
+
+**Description**
+
+The `inspect` command allows you to determine the container for each process in a pipeline without running the pipeline. It prints to stdout a listing of containers for each process, formatted either as JSON or Nextflow configuration.
+
+**Options**
+
+`-concretize`
+: Build the container images resolved by the inspect command.
+
+`-format` (`json`)
+: Inspect output format. Can be `json` or `config`.
+
+`-i, -ignore-errors`
+: Ignore errors while inspecting the pipeline.
+
+`-params-file`
+: Load script parameters from a JSON/YAML file.
+
+`-profile`
+: Use the given configuration profile(s).
+
+`-r, revision`
+: Revision of the project to inspect (either a git branch, tag or commit SHA number).
+
+**Examples**
+
+Get the list of containers used by a pipeline.
+
+```console
+$ nextflow inspect nextflow-io/hello
+```
+
+Specify parameters as with the `run` command:
+
+```console
+$ nextflow inspect main.nf --alpha 1 --beta foo
+```
+
+### `kuberun`
+
+Launch a Nextflow pipeline on a Kubernetes cluster.
+
+**Usage**
+
+```console
+$ nextflow kuberun [options] [project]
+```
+
+**Description**
+
+The `kuberun` command builds upon the `run` command and offers a deep integration with the Kubernetes execution environment. This command deploys the Nextflow runtime as a Kubernetes pod and assumes that you've already installed the `kubectl` CLI. The `kuberun` command does not allow the execution of local Nextflow scripts. See {ref}`k8s-page` for more information.
+
+**Options**
+
+The `kuberun` command supports the following options from [`run`](#run):
+
+- `-cache`
+- `-disable-jobs-cancellation`
+- `-dsl1`
+- `-dsl2`
+- `-dump-channels`
+- `-dump-hashes`
+- `-e.<key>=<value>`
+- `-entry`
+- `-h, -help`
+- `-hub`
+- `-latest`
+- `-main-script`
+- `-name`
+- `-offline`
+- `-params-file`
+- `-plugins`
+- `-preview`
+- `-process.<key>=<value>`
+- `-profile`
+- `-qs, -queue-size`
+- `-resume`
+- `-r, -revision`
+- `-stub, -stub-run`
+- `-user`
+- `-with-conda`
+- `-with-dag`
+- `-N, -with-notification`
+- `-with-report`
+- `-with-spack`
+- `-with-timeline`
+- `-with-tower`
+- `-with-trace`
+- `-with-wave`
+- `-with-weblog`
+- `-without-spack`
+- `-without-wave`
+- `-w, -work-dir`
+
+The following new options are also available:
+
+`-head-cpus`
+: :::{versionadded} 22.01.0-edge
+  :::
+: Specify number of CPUs requested for the Nextflow pod.
+
+`-head-image`
+: :::{versionadded} 22.07.1-edge
+  :::
+: Specify the container image for the Nextflow driver pod.
+
+`-head-memory`
+: :::{versionadded} 22.01.0-edge
+  :::
+: Specify amount of memory requested for the Nextflow pod.
+
+`-head-prescript`
+: :::{versionadded} 22.05.0-edge
+  :::
+: Specify script to be run before the Nextflow pod starts.
+
+`-n, -namespace`
+: Specify the K8s namespace to use.
+
+`-remoteConfig`
+: Add the specified file from the K8s cluster to configuration set.
+
+`-remoteProfile`
+: Choose a configuration profile in the remoteConfig.
+
+`-v, -volume-mount`
+: Volume claim mounts, e.g. `my-pvc:/mnt/path`.
+
+**Examples**
+
+Execute a pipeline into a Kubernetes cluster.
+
+```console
+$ nextflow kuberun nextflow-io/hello
+```
+
+### `list`
+
+List all downloaded projects.
+
+**Usage**
+
+```console
+$ nextflow list [options]
+```
+
+**Description**
+
+The `list` commands prints a list of the projects which are already downloaded into the global cache `~/.nextflow/assets`.
+
+**Options**
+
+`-h, -help`
+: Print the command usage.
+
+**Examples**
+
+List the downloaded pipelines.
+
+```console
+$ nextflow list
+
+nextflow-io/hello
+nextflow-hub/fastqc
+```
+
+(cli-log)=
+
+### `log`
+
+Print the execution history and log information.
+
+**Usage**
+
+```console
+$ nextflow log [options] [run_name | session_id]
+```
+
+**Description**
+
+The `log` command is used to query the execution metadata associated with pipelines executed by Nextflow. The list of executed pipelines can be generated by running `nextflow log`. Instead of run name, it's also possible to use a session id. Moreover, this command contains multiple options to facilitate the queries and is especially useful while debugging a pipeline and while inspecting pipeline execution metadata.
+
+**Options**
+
+`-after`
+: Show log entries for runs executed *after* the specified one.
+
+`-before`
+: Show log entries for runs executed *before* the specified one.
+
+`-but`
+: Show log entries for runs executed *but* the specified one.
+
+`-f, -fields`
+: Comma-separated list of fields to include in the printed log. Use the `-l` option to see the list of available fields.
+
+`-F, -filter`
+: Filter log entries by a custom expression, e.g. `process =~ /foo.*/ && status == 'COMPLETED'`.
+
+`-h, -help`
+: Print the command usage.
+
+`-l, -list-fields`
+: Show all available fields.
+
+`-quiet`
+: Show only run names.
+
+`-s`
+: Character used to separate column values.
+
+`-t, -template`
+: Text template used to each record in the log.
+
+**Examples**
+
+Listing the execution logs of previous invocations of all pipelines in a project.
+
+```console
+$ nextflow log
+
+TIMESTAMP           DURATION        RUN NAME        STATUS  REVISION ID     SESSION ID                              COMMAND
+2020-10-07 11:52:24 2.1s            focused_payne   OK      96eb04d6a4      af6adaaa-ad4f-48a2-9f6a-b121e789adf5    nextflow run nextflow-io/hello -r master
+2020-10-07 11:53:00 3.1s            tiny_leavitt    OK      e3b475a61b      4d3b95c5-4385-42b6-b430-c865a70d56a4    nextflow run ./tutorial.nf
+2020-10-07 11:53:29 2.5s            boring_euler    OK      e3b475a61b      a6276975-7173-4208-ae09-ab9d6dce8737    nextflow run tutorial.nf
+```
+
+Listing only the *run names* of the execution logs of all pipelines invocations in a project.
+
+```console
+$ nextflow log -quiet
+
+focused_payne
+tiny_leavitt
+boring_euler
+```
+
+List the execution entries *only* a specific execution.
+
+```console
+$ nextflow log tiny_leavitt
+
+work/1f/f1ea9158fb23b53d5083953121d6b6
+work/bf/334115deec60929dc18edf0010032a
+work/a3/06521d75da296d4dd7f4f8caaddad8
+```
+
+List the execution entries *after* a specific execution.
+
+```console
+$ nextflow log -after tiny_leavitt
+
+work/92/c1a9cd9a96e0531d81ca69f5dc3bb7
+work/3f/70944c7a549b6221e1ccc7b4b21b62
+work/0e/2ebdba85f76f6068b21a1bcbf10cab
+```
+
+List the execution entries *before* a specific execution.
+
+```console
+$ nextflow log -before tiny_leavitt
+
+work/5d/ad76f7b7ab3500cf616814ef644b61
+work/c4/69a82b080a477612ba8d8e4c27b579
+work/be/a4fa2aa38f76fd324958c81c2e4603
+work/54/39116773891c47a91e3c1733aad4de
+```
+
+List the execution entries *except* for a specific execution.
+
+```console
+$ nextflow log -but tiny_leavitt
+
+work/5d/ad76f7b7ab3500cf616814ef644b61
+work/c4/69a82b080a477612ba8d8e4c27b579
+work/be/a4fa2aa38f76fd324958c81c2e4603
+work/54/39116773891c47a91e3c1733aad4de
+```
+
+Filter specific fields from the execution log of a process.
+
+```console
+$ nextflow log tiny_leavitt -f 'process,exit,hash,duration'
+
+splitLetters        0       1f/f1ea91       112ms
+convertToUpper      0       bf/334115       144ms
+convertToUpper      0       a3/06521d       139ms
+```
+
+Filter fields from the execution log of a process based on a criteria.
+
+```console
+$ nextflow log tiny_leavitt -F 'process =~ /splitLetters/'
+
+work/1f/f1ea9158fb23b53d5083953121d6b6
+```
+
+(cli-plugin)=
+
+### `plugin`
+
+Manage plugins and run plugin-specific commands.
+
+```console
+$ nextflow plugin <subcommand> [options]
+```
+
+The `plugin` command provides several subcommands for managing and using plugins:
+
+`install <plugin[@version],..>`
+
+: Install a plugin. Multiple plugins can be specified as a comma-separated list. Each plugin id consists of a name and optional version separated by a `@`.
+
+`<plugin>:<subcommand> [options]`
+
+: Execute a plugin-specific command.
+
+### `pull`
+
+Download or update a project.
+
+**Usage**
+
+```console
+$ nextflow pull [options] [project]
+```
+
+**Description**
+
+The `pull` command downloads a pipeline from a Git-hosting platform into the global cache `~/.nextflow/assets` and modifies it accordingly. For downloading a pipeline into a local directory, please refer to the `nextflow clone` command.
+
+**Options**
+
+`-all`
+: Update all downloaded projects.
+
+`-d, -deep`
+: Create a shallow clone of the specified depth.
+
+`-h, -help`
+: Print the command usage.
+
+`-hub` (`github`)
+: Service hub where the project is hosted. Options: `gitlab` or `bitbucket`
+
+`-r, -revision`
+: Revision of the project to run (either a git branch, tag or commit hash).
+: When passing a git tag or branch, the `workflow.revision` and `workflow.commitId` fields are populated. When passing only the commit hash, `workflow.revision` is not defined.
+
+`-user`
+: Private repository user name.
+
+**Examples**
+
+Download a new pipeline or pull the latest revision for a specific project.
+
+```console
+$ nextflow pull nextflow-io/hello
+
+Checking nextflow-io/hello ...
+done - revision: 96eb04d6a4 [master]
+```
+
+Pull the latest revision for all downloaded projects.
+
+```console
+$ nextflow pull -all
+
+Checking nextflow-io/hello ...
+done - revision: 96eb04d6a4 [master]
+Checking nextflow-hub/fastqc ...
+done - revision: 087659b18e [master]
+```
+
+Download a specific revision of a new project or pull the latest revision for a specific project.
+
+```console
+$ nextflow pull nextflow-io/hello -r v1.1
+
+Checking nextflow-io/hello ...
+checkout-out at AnyObjectId[1c3e9e7404127514d69369cd87f8036830f5cf64] - revision: 1c3e9e7404 [v1.1]
+```
+
+(cli-run)=
+
+### `run`
+
+Execute a pipeline.
+
+**Usage**
+
+```console
+$ nextflow run [options] [project]
+```
+
+**Description**
+
+The `run` command is used to execute a local pipeline script or remote pipeline project.
+
+**Options**
+
+`-E`
+: Exports all current system environment.
+
+`-ansi-log`
+: Enable/disable ANSI console logging.
+
+`-bucket-dir`
+: Remote bucket where intermediate result files are stored. When running a hybrid workflow, `-bucket-dir` and `-work-dir` should define separate work directories for remote tasks and local tasks, respectively.
+
+`-cache`
+: Enable/disable processes caching.
+
+`-d, -deep`
+: Create a shallow clone of the specified depth.
+
+`-disable-jobs-cancellation`
+: Prevent the cancellation of child jobs on execution termination
+
+`-dsl1`
+: :::{deprecated} 23.09.0-edge
+  :::
+: Execute the workflow using DSL1 syntax.
+
+`-dsl2`
+: :::{deprecated} 23.09.0-edge
+  :::
+: Execute the workflow using DSL2 syntax.
+
+`-dump-channels`
+: Dump channels for debugging purpose.
+
+`-dump-hashes`
+: Dump task hash keys for debugging purposes.
+: :::{versionadded} 23.10.0
+  You can use `-dump-hashes json` to dump the task hash keys as JSON for easier post-processing. See the {ref}`caching and resuming tips <cache-compare-hashes>` for more details.
+  :::
+
+`-e.<key>=<value>`
+: Add the specified variable to execution environment.
+
+`-entry`
+: :::{deprecated} 24.10.0
+  Use params in the entry workflow to call different workflows from the command line.
+  :::
+: Entry workflow to be executed.
+
+`-h, -help`
+: Print the command usage.
+
+`-hub` (`github`)
+: Service hub where the project is hosted. Options: `gitlab` or `bitbucket`
+
+`-latest`
+: Pull latest changes before run.
+
+`-lib`
+: Library extension path.
+
+`-main-script` (`main.nf`)
+: :::{versionadded} 20.09.1-edge
+  :::
+: The script file to be executed when launching a project directory or repository.
+
+`-name`
+: Assign a mnemonic name to the a pipeline run.
+
+`-offline`
+: Do not check for remote project updates.
+
+`-o, -output-dir` (`results`)
+: :::{versionadded} 24.10.0
+  :::
+: Directory where workflow outputs are stored.
+
+`-params-file`
+: Load script parameters from a JSON/YAML file.
+
+`-plugins`
+: Comma separated list of plugin ids to be applied in the pipeline execution.
+
+`-preview`
+: :::{versionadded} 22.06.0-edge
+  :::
+: Run the workflow script skipping the execution of all processes.
+
+`-process.<key>=<value>`
+: Set process config options.
+
+`-profile`
+: Choose a configuration profile.
+
+`-qs, -queue-size`
+: Max number of processes that can be executed in parallel by each executor.
+
+`-resume`
+: Execute the script using the cached results, useful to continue executions that was stopped by an error.
+
+`-r, -revision`
+: Revision of the project to run (either a git branch, tag or commit hash).
+: When passing a git tag or branch, the `workflow.revision` and `workflow.commitId` fields are populated. When passing only the commit hash, `workflow.revision` is not defined.
+
+`-stub-run, -stub`
+: Execute the workflow replacing process scripts with command stubs
+
+`-test`
+: Test a script function with the name specified.
+
+`-user`
+: Private repository user name.
+
+`-with-apptainer`
+: Enable process execution in an Apptainer container.
+
+`-with-charliecloud`
+: Enable process execution in a Charliecloud container.
+
+`-with-cloudcache`
+: Enable the use of the Cloud cache plugin for storing cache metadata to an object storage bucket.
+
+`-with-conda`
+: Use the specified Conda environment package or file (must end with `.yml` or `.yaml`)
+
+`-with-dag` (`dag-<timestamp>.html`)
+: Create pipeline DAG file.
+: :::{versionchanged} 23.10.0
+  The default format was changed from `dot` to `html`.
+  :::
+
+`-with-docker`
+: Enable process execution in a Docker container.
+
+`-N, -with-notification`
+: Send a notification email on workflow completion to the specified recipients.
+
+`-with-podman`
+: Enable process execution in a Podman container.
+
+`-with-report` (`report-<timestamp>.html`)
+: Create workflow execution HTML report.
+
+`-with-singularity`
+: Enable process execution in a Singularity container.
+
+`-with-spack`
+: Use the specified Spack environment package or file (must end with `.yaml`)
+
+`-with-timeline` (`timeline-<timestamp>.html`)
+: Create workflow execution timeline.
+
+`-with-tower` (`https://api.cloud.seqera.io`)
+: Monitor workflow execution with [Seqera Platform](https://seqera.io/) (formerly Tower Cloud).
+
+`-with-trace` (`trace-<timestamp>.txt`)
+: Create workflow execution trace file.
+
+`-with-wave` (`https://wave.seqera.io`)
+: Enable the use of Wave containers.
+
+`-with-weblog` (`http://localhost`)
+: Send workflow status messages via HTTP to target URL.
+
+`-without-conda`
+: Disable process execution with Conda.
+
+`-without-docker`
+: Disable process execution with Docker.
+
+`-without-podman`
+: Disable process execution in a Podman container.
+
+`-without-spack`
+: Disable process execution with Spack.
+
+`-without-wave`
+: Disable the use of Wave containers.
+
+`-w, -work-dir` (`work`)
+: Directory where intermediate result files are stored.
+
+**Examples**
+
+- Run a specific revision of a remote pipeline.
+
+  ```console
+  $ nextflow run nextflow-io/hello -r v1.1
+
+  N E X T F L O W  ~  version 20.07.1
+  Launching `nextflow-io/hello` [grave_cajal] - revision: 1c3e9e7404 [v1.1]
+  ```
+
+- Choose a `profile` for running the project. Assumes that a profile named `docker` has already been defined in the config file.
+
+  ```console
+  $ nextflow run main.nf -profile docker
+  ```
+
+- Execute a pipeline and generate the summary HTML report. For more information on the metrics, please refer the {ref}`tracing-page` section:
+
+  ```console
+  $ nextflow run main.nf -with-report
+  ```
+
+- Execute a pipeline with a custom queue size. By default, the queue size is the number of available CPUs.
+
+  ```console
+  $ nextflow run nextflow-io/hello -qs 4
+  ```
+
+- Invoke the pipeline with a specific workflow as the entry-point.
+
+  ```console
+  $ nextflow run main.nf -entry workflow_A
+  ```
+
+- Execute a pipeline with integrated monitoring in [Seqera Platform](https://seqera.io).
+
+  ```console
+  $ nextflow run nextflow-io/hello -with-tower
+  ```
+
+- Execute a pipeline with a custom parameters file (YAML or JSON).
+
+  ```console
+  $ nextflow run main.nf -params-file pipeline_params.yml
+  ```
+
+  See {ref}`cli-params` for more information about writing custom parameters files.
+
+### `self-update`
+
+Update the nextflow runtime to the latest available version.
+
+**Usage**
+
+```console
+$ nextflow self-update
+```
+
+**Description**
+
+The `self-update` command directs the `nextflow` CLI to update itself to the latest stable release.
+
+**Examples**
+
+Update Nextflow.
+
+```console
+$ nextflow self-update
+
+      N E X T F L O W
+      version 20.07.1 build 5412
+      created 24-07-2020 15:18 UTC (20:48 IDT)
+      cite doi:10.1038/nbt.3820
+      http://nextflow.io
+
+
+Nextflow installation completed. Please note:
+- the executable file `nextflow` has been created in the folder: /usr/local/bin
+```
+
+### `view`
+
+View a project's script file(s).
+
+**Usage**
+
+```console
+$ nextflow view [options] [project]
+```
+
+**Description**
+
+The `view` command is used to inspect the pipelines that are already stored in the global nextflow cache. For downloading a pipeline into the global cache `~/.nextflow/assets`, refer to the `pull` command.
+
+**Options**
+
+`-h, -help`
+: Print the command usage.
+
+`-l`
+: List repository content.
+
+`-q`
+: Hide header line.
+
+**Examples**
+
+Viewing the contents of a downloaded pipeline.
+
+```console
+$ nextflow view nextflow-io/hello
+
+== content of file: .nextflow/assets/nextflow-io/hello/main.nf
+#!/usr/bin/env nextflow
+
+process sayHello {
+  input:
+    val x
+  output:
+    stdout
+  script:
+    """
+    echo '$x world!'
+    """
+}
+
+workflow {
+  Channel.of('Bonjour', 'Ciao', 'Hello', 'Hola') | sayHello | view
+}
+```
+
+List the folder structure of the downloaded pipeline:
+
+```console
+$ nextflow view -l nextflow-io/hello
+
+== content of path: .nextflow/assets/nextflow-io/hello
+LICENSE
+README.md
+nextflow.config
+.gitignore
+circle.yml
+foo.nf
+.git
+.travis.yml
+main.nf
+```
+
+View the contents of a downloaded pipeline without omitting the header:
+
+```console
+$ nextflow view -q nextflow-io/hello
+
+#!/usr/bin/env nextflow
+
+process sayHello {
+  input:
+    val x
+  output:
+    stdout
+  script:
+    """
+    echo '$x world!'
+    """
+}
+
+workflow {
+  Channel.of('Bonjour', 'Ciao', 'Hello', 'Hola') | sayHello | view
+}
+```
diff --git a/docs/reference/config.md b/docs/reference/config.md
new file mode 100644
index 0000000000..0efb1ce6ae
--- /dev/null
+++ b/docs/reference/config.md
@@ -0,0 +1,1721 @@
+(config-options)=
+
+# Configuration options
+
+This page lists all of the available settings in the {ref}`Nextflow configuration <config-page>`.
+
+(config-unscoped)=
+
+## Unscoped options
+
+`cleanup`
+: If `true`, on a successful completion of a run all files in *work* directory are automatically deleted.
+
+  :::{warning}
+  The use of the `cleanup` option will prevent the use of the *resume* feature on subsequent executions of that pipeline run. Also, be aware that deleting all scratch files can take a lot of time, especially when using a shared file system or remote cloud storage.
+  :::
+
+`dumpHashes`
+: If `true`, dump task hash keys in the log file, for debugging purposes. Equivalent to the `-dump-hashes` option of the `run` command.
+
+`outputDir`
+: :::{versionadded} 24.10.0
+  :::
+: Defines the pipeline output directory. Equivalent to the `-output-dir` option of the `run` command.
+
+`resume`
+: If `true`, enable the use of previously cached task executions. Equivalent to the `-resume` option of the `run` command.
+
+`workDir`
+: Defines the pipeline work directory. Equivalent to the `-work-dir` option of the `run` command.
+
+(config-apptainer)=
+
+## `apptainer`
+
+The `apptainer` scope controls how [Apptainer](https://apptainer.org) containers are executed by Nextflow.
+
+The following settings are available:
+
+`apptainer.autoMounts`
+: When `true` Nextflow automatically mounts host paths in the executed container. It requires the `user bind control` feature to be enabled in your Apptainer installation (default: `true`).
+
+`apptainer.cacheDir`
+: The directory where remote Apptainer images are stored. When using a computing cluster it must be a shared folder accessible to all compute nodes.
+
+`apptainer.enabled`
+: Enable Apptainer execution (default: `false`).
+
+`apptainer.engineOptions`
+: This attribute can be used to provide any option supported by the Apptainer engine i.e. `apptainer [OPTIONS]`.
+
+`apptainer.envWhitelist`
+: Comma separated list of environment variable names to be included in the container environment.
+
+`apptainer.libraryDir`
+: Directory where remote Apptainer images are retrieved. When using a computing cluster it must be a shared folder accessible to all compute nodes.
+
+`apptainer.noHttps`
+: Pull the Apptainer image with http protocol (default: `false`).
+
+`apptainer.ociAutoPull`
+: :::{versionadded} 23.12.0-edge
+  :::
+: When enabled, OCI (and Docker) container images are pulled and converted to the SIF format by the Apptainer run command, instead of Nextflow (default: `false`).
+
+  :::{note}
+  Leave `ociAutoPull` disabled if you are willing to build a Singularity/Apptainer native image with Wave (see the {ref}`wave-singularity` section).
+  :::
+
+`apptainer.pullTimeout`
+: The amount of time the Apptainer pull can last, exceeding which the process is terminated (default: `20 min`).
+
+`apptainer.registry`
+: The registry from where Docker images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
+
+`apptainer.runOptions`
+: This attribute can be used to provide any extra command line options supported by `apptainer exec`.
+
+Read the {ref}`container-apptainer` page to learn more about how to use Apptainer containers with Nextflow.
+
+(config-aws)=
+
+## `aws`
+
+The `aws` scope controls the interactions with AWS, including AWS Batch and S3. For example:
+
+```groovy
+aws {
+    accessKey = '<YOUR S3 ACCESS KEY>'
+    secretKey = '<YOUR S3 SECRET KEY>'
+    region = 'us-east-1'
+
+    client {
+        maxConnections = 20
+        connectionTimeout = 10000
+        uploadStorageClass = 'INTELLIGENT_TIERING'
+        storageEncryption = 'AES256'
+    }
+    batch {
+        cliPath = '/home/ec2-user/miniconda/bin/aws'
+        maxTransferAttempts = 3
+        delayBetweenAttempts = '5 sec'
+    }
+}
+```
+
+:::{tip}
+This scope can also be used to configure access to S3-compatible storage outside of AWS, such as [Ceph](https://ceph.com/en/) and [MinIO](https://min.io/).
+:::
+
+Read the {ref}`aws-page` and {ref}`amazons3-page` pages for more information.
+
+The following settings are available:
+
+`aws.accessKey`
+: AWS account access key
+
+`aws.profile`
+: :::{versionadded} 22.12.0-edge
+  :::
+: AWS profile from `~/.aws/credentials`
+
+`aws.region`
+: AWS region (e.g. `us-east-1`)
+
+`aws.secretKey`
+: AWS account secret key
+
+`aws.batch.cliPath`
+: The path where the AWS command line tool is installed in the host AMI.
+
+`aws.batch.delayBetweenAttempts`
+: Delay between download attempts from S3 (default: `10 sec`).
+
+`aws.batch.executionRole`
+: :::{versionadded} 23.12.0-edge
+  :::
+: The AWS Batch Execution Role ARN that needs to be used to execute the Batch Job. This is mandatory when using AWS Fargate platform type. See [AWS documentation](https://docs.aws.amazon.com/batch/latest/userguide/execution-IAM-role.html) for more details.
+
+`aws.batch.jobRole`
+: The AWS Batch Job Role ARN that needs to be used to execute the Batch Job.
+
+`aws.batch.logsGroup`
+: :::{versionadded} 22.09.0-edge
+  :::
+: The name of the logs group used by Batch Jobs (default: `/aws/batch/job`).
+
+`aws.batch.maxParallelTransfers`
+: Max parallel upload/download transfer operations *per job* (default: `4`).
+
+`aws.batch.maxSpotAttempts`
+: :::{versionadded} 22.04.0
+  :::
+: :::{versionchanged} 24.08.0-edge
+  The default value was changed from `5` to `0`.
+  :::
+: Max number of execution attempts of a job interrupted by a EC2 spot reclaim event (default: `0`)
+
+`aws.batch.maxTransferAttempts`
+: Max number of downloads attempts from S3 (default: `1`).
+
+`aws.batch.platformType`
+: :::{versionadded} 23.12.0-edge
+  :::
+: Allow specifying the compute platform type used by AWS Batch, that can be either `ec2` or `fargate`. See AWS documentation to learn more about [AWS Fargate platform type](https://docs.aws.amazon.com/batch/latest/userguide/fargate.html) for AWS Batch.
+
+`aws.batch.retryMode`
+: The retry mode configuration setting, to accommodate rate-limiting on [AWS services](https://docs.aws.amazon.com/cli/latest/userguide/cli-configure-retries.html) (default: `standard`, other options: `legacy`, `adaptive`); this handling is delegated to AWS. To have Nextflow handle retries instead, use `built-in`.
+
+`aws.batch.schedulingPriority`
+: :::{versionadded} 23.01.0-edge
+  :::
+: The scheduling priority for all tasks when using [fair-share scheduling for AWS Batch](https://aws.amazon.com/blogs/hpc/introducing-fair-share-scheduling-for-aws-batch/) (default: `0`)
+
+`aws.batch.shareIdentifier`
+: :::{versionadded} 22.09.0-edge
+  :::
+: The share identifier for all tasks when using [fair-share scheduling for AWS Batch](https://aws.amazon.com/blogs/hpc/introducing-fair-share-scheduling-for-aws-batch/)
+
+`aws.batch.volumes`
+: One or more container mounts. Mounts can be specified as simple e.g. `/some/path` or canonical format e.g. `/host/path:/mount/path[:ro|rw]`. Multiple mounts can be specified separating them with a comma or using a list object.
+
+`aws.client.anonymous`
+: Allow the access of public S3 buckets without the need to provide AWS credentials. Any service that does not accept unsigned requests will return a service access error.
+
+`aws.client.s3Acl`
+: Allow the setting of predefined bucket permissions, also known as *canned ACL*. Permitted values are `Private`, `PublicRead`, `PublicReadWrite`, `AuthenticatedRead`, `LogDeliveryWrite`, `BucketOwnerRead`, `BucketOwnerFullControl`, and `AwsExecRead`. See [Amazon docs](https://docs.aws.amazon.com/AmazonS3/latest/userguide/acl-overview.html#canned-acl) for details.
+
+`aws.client.connectionTimeout`
+: The amount of time to wait (in milliseconds) when initially establishing a connection before timing out.
+
+`aws.client.endpoint`
+: The AWS S3 API entry point e.g. `https://s3-us-west-1.amazonaws.com`. Note: the endpoint must include the protocol prefix e.g. `https://`.
+
+`aws.client.glacierAutoRetrieval`
+: :::{deprecated} 24.02.0-edge
+  Glacier auto-retrieval is no longer supported. Instead, consider using the AWS CLI to restore any Glacier objects before or at the beginning of your pipeline (i.e. in a Nextflow process).
+  :::
+: Enable auto retrieval of S3 objects with a Glacier storage class (default: `false`).
+
+`aws.client.glacierExpirationDays`
+: :::{deprecated} 24.02.0-edge
+  :::
+: The time, in days, between when an object is restored to the bucket and when it expires (default: `7`).
+
+`aws.client.glacierRetrievalTier`
+: :::{deprecated} 24.02.0-edge
+  :::
+: The retrieval tier to use when restoring objects from Glacier, one of [`Expedited`, `Standard`, `Bulk`].
+
+`aws.client.maxConnections`
+: The maximum number of allowed open HTTP connections.
+
+`aws.client.maxErrorRetry`
+: The maximum number of retry attempts for failed retryable requests.
+
+`aws.client.protocol`
+: The protocol (i.e. HTTP or HTTPS) to use when connecting to AWS.
+
+`aws.client.proxyHost`
+: The proxy host to connect through.
+
+`aws.client.proxyPort`
+: The port on the proxy host to connect through.
+
+`aws.client.proxyUsername`
+: The user name to use when connecting through a proxy.
+
+`aws.client.proxyPassword`
+: The password to use when connecting through a proxy.
+
+`aws.client.requesterPays`
+: :::{versionadded} 24.05.0-edge
+  :::
+: Enable the requester pays feature for S3 buckets.
+
+`aws.client.s3PathStyleAccess`
+: Enable the use of path-based access model that is used to specify the address of an object in S3-compatible storage systems.
+
+`aws.client.signerOverride`
+: The name of the signature algorithm to use for signing requests made by the client.
+
+`aws.client.socketSendBufferSizeHint`
+: The Size hint (in bytes) for the low level TCP send buffer.
+
+`aws.client.socketRecvBufferSizeHint`
+: The Size hint (in bytes) for the low level TCP receive buffer.
+
+`aws.client.socketTimeout`
+: The amount of time to wait (in milliseconds) for data to be transferred over an established, open connection before the connection is timed out.
+
+`aws.client.storageEncryption`
+: The S3 server side encryption to be used when saving objects on S3, either `AES256` or `aws:kms` values are allowed.
+
+`aws.client.storageKmsKeyId`
+: :::{versionadded} 22.05.0-edge
+  :::
+: The AWS KMS key Id to be used to encrypt files stored in the target S3 bucket.
+
+`aws.client.userAgent`
+: The HTTP user agent header passed with all HTTP requests.
+
+`aws.client.uploadChunkSize`
+: The size of a single part in a multipart upload (default: `100 MB`).
+
+`aws.client.uploadMaxAttempts`
+: The maximum number of upload attempts after which a multipart upload returns an error (default: `5`).
+
+`aws.client.uploadMaxThreads`
+: The maximum number of threads used for multipart upload.
+
+`aws.client.uploadRetrySleep`
+: The time to wait after a failed upload attempt to retry the part upload (default: `500ms`).
+
+`aws.client.uploadStorageClass`
+: The S3 storage class applied to stored objects, one of \[`STANDARD`, `STANDARD_IA`, `ONEZONE_IA`, `INTELLIGENT_TIERING`\] (default: `STANDARD`).
+
+(config-azure)=
+
+## `azure`
+
+The `azure` scope allows you to configure the interactions with Azure, including Azure Batch and Azure Blob Storage.
+
+Read the {ref}`azure-page` page for more information.
+
+The following settings are available:
+
+`azure.activeDirectory.servicePrincipalId`
+: The service principal client ID
+
+`azure.activeDirectory.servicePrincipalSecret`
+: The service principal client secret
+
+`azure.activeDirectory.tenantId`
+: The Azure tenant ID
+
+`azure.batch.accountName`
+: The batch service account name.
+
+`azure.batch.accountKey`
+: The batch service account key.
+
+`azure.batch.allowPoolCreation`
+: Enable the automatic creation of batch pools specified in the Nextflow configuration file (default: `false`).
+
+`azure.batch.autoPoolMode`
+: Enable the automatic creation of batch pools depending on the pipeline resources demand (default: `true`).
+
+`azure.batch.copyToolInstallMode`
+: Specify where the `azcopy` tool used by Nextflow. When `node` is specified it's copied once during the pool creation. When `task` is provider, it's installed for each task execution. Finally when `off` is specified, the `azcopy` tool is not installed (default: `node`).
+
+`azure.batch.deleteJobsOnCompletion`
+: Delete all jobs when the workflow completes (default: `false`).
+: :::{versionchanged} 23.08.0-edge
+  Default value was changed from `true` to `false`.
+  :::
+
+`azure.batch.deletePoolsOnCompletion`
+: Delete all compute node pools when the workflow completes (default: `false`).
+
+`azure.batch.deleteTasksOnCompletion`
+: :::{versionadded} 23.08.0-edge
+  :::
+: Delete each task when it completes (default: `true`).
+: Although this setting is enabled by default, failed tasks will not be deleted unless it is explicitly enabled. This way, the default behavior is that successful tasks are deleted while failed tasks are preserved for debugging purposes.
+
+`azure.batch.endpoint`
+: The batch service endpoint e.g. `https://nfbatch1.westeurope.batch.azure.com`.
+
+`azure.batch.location`
+: The name of the batch service region, e.g. `westeurope` or `eastus2`. This is not needed when the endpoint is specified.
+
+`azure.batch.terminateJobsOnCompletion`
+: :::{versionadded} 23.05.0-edge
+  :::
+: When the workflow completes, set all jobs to terminate on task completion. (default: `true`).
+
+`azure.batch.pools.<name>.autoScale`
+: Enable autoscaling feature for the pool identified with `<name>`.
+
+`azure.batch.pools.<name>.fileShareRootPath`
+: If mounting File Shares, this is the internal root mounting point. Must be `/mnt/resource/batch/tasks/fsmounts` for CentOS nodes or `/mnt/batch/tasks/fsmounts` for Ubuntu nodes (default is for CentOS).
+
+`azure.batch.pools.<name>.lowPriority`
+: Enable the use of low-priority VMs (default: `false`).
+
+`azure.batch.pools.<name>.maxVmCount`
+: Specify the max of virtual machine when using auto scale option.
+
+`azure.batch.pools.<name>.mountOptions`
+: Specify the mount options for mounting the file shares (default: `-o vers=3.0,dir_mode=0777,file_mode=0777,sec=ntlmssp`).
+
+`azure.batch.pools.<name>.offer`
+: Specify the offer type of the virtual machine type used by the pool identified with `<name>` (default: `centos-container`).
+
+`azure.batch.pools.<name>.privileged`
+: Enable the task to run with elevated access. Ignored if `runAs` is set (default: `false`).
+
+`azure.batch.pools.<name>.publisher`
+: Specify the publisher of virtual machine type used by the pool identified with `<name>` (default: `microsoft-azure-batch`).
+
+`azure.batch.pools.<name>.runAs`
+: Specify the username under which the task is run. The user must already exist on each node of the pool.
+
+`azure.batch.pools.<name>.scaleFormula`
+: Specify the scale formula for the pool identified with `<name>`. See Azure Batch [scaling documentation](https://docs.microsoft.com/en-us/azure/batch/batch-automatic-scaling) for details.
+
+`azure.batch.pools.<name>.scaleInterval`
+: Specify the interval at which to automatically adjust the Pool size according to the autoscale formula. The minimum and maximum value are 5 minutes and 168 hours respectively (default: `10 mins`).
+
+`azure.batch.pools.<name>.schedulePolicy`
+: Specify the scheduling policy for the pool identified with `<name>`. It can be either `spread` or `pack` (default: `spread`).
+
+`azure.batch.pools.<name>.sku`
+: Specify the ID of the Compute Node agent SKU which the pool identified with `<name>` supports (default: `batch.node.centos 8`).
+
+`azure.batch.pools.<name>.startTask.script`
+: :::{versionadded} 24.03.0-edge
+  :::
+: Specify the `startTask` that is executed as the node joins the Azure Batch node pool.
+
+`azure.batch.pools.<name>.startTask.privileged`
+: :::{versionadded} 24.03.0-edge
+  :::
+: Enable the `startTask` to run with elevated access (default: `false`).
+
+`azure.batch.pools.<name>.virtualNetwork`
+: :::{versionadded} 23.03.0-edge
+  :::
+: Specify the subnet ID of a virtual network in which to create the pool.
+
+`azure.batch.pools.<name>.vmCount`
+: Specify the number of virtual machines provisioned by the pool identified with `<name>`.
+
+`azure.batch.pools.<name>.vmType`
+: Specify the virtual machine type used by the pool identified with `<name>`.
+
+`azure.managedIdentity.clientId`
+: Specify the client ID for an Azure [managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/overview). See {ref}`azure-managed-identities` for more details.
+
+`azure.managedIdentity.system`
+: When `true`, use the system-assigned [managed identity](https://learn.microsoft.com/en-us/entra/identity/managed-identities-azure-resources/overview) to authenticate Azure resources. See {ref}`azure-managed-identities` for more details.
+
+`azure.managedIdentity.tenantId`
+: The Azure tenant ID
+
+`azure.registry.server`
+: Specify the container registry from which to pull the Docker images (default: `docker.io`).
+
+`azure.registry.userName`
+: Specify the username to connect to a private container registry.
+
+`azure.registry.password`
+: Specify the password to connect to a private container registry.
+
+`azure.retryPolicy.delay`
+: Delay when retrying failed API requests (default: `500ms`).
+
+`azure.retryPolicy.jitter`
+: Jitter value when retrying failed API requests (default: `0.25`).
+
+`azure.retryPolicy.maxAttempts`
+: Max attempts when retrying failed API requests (default: `10`).
+
+`azure.retryPolicy.maxDelay`
+: Max delay when retrying failed API requests (default: `90s`).
+
+`azure.storage.accountName`
+: The blob storage account name
+
+`azure.storage.accountKey`
+: The blob storage account key
+
+`azure.storage.sasToken`
+: The blob storage shared access signature token. This can be provided as an alternative to the `accountKey` setting.
+
+`azure.storage.tokenDuration`
+: The duration of the shared access signature token created by Nextflow when the `sasToken` option is *not* specified (default: `48h`).
+
+(config-charliecloud)=
+
+## `charliecloud`
+
+The `charliecloud` scope controls how [Charliecloud](https://hpc.github.io/charliecloud/) containers are executed by Nextflow.
+
+The following settings are available:
+
+`charliecloud.enabled`
+: Enable Charliecloud execution (default: `false`).
+
+`charliecloud.writeFake`
+: Enable `writeFake` with charliecloud (default: `true`) This allows to run containers from storage in writeable mode, using overlayfs. `writeFake` requires unprivileged `overlayfs` (Linux kernel >= 5.11). For full support, tempfs with xattrs in the user namespace (Linux kernel >= 6.6) is required, see [charliecloud documentation](https://hpc.github.io/charliecloud/ch-run.html#ch-run-overlay) for details.
+
+`charliecloud.cacheDir`
+: The directory where remote Charliecloud images are stored. When using a computing cluster it must be a shared folder accessible to all compute nodes.
+
+`charliecloud.envWhitelist`
+: Comma separated list of environment variable names to be included in the container environment.
+
+`charliecloud.pullTimeout`
+: The amount of time the Charliecloud pull can last, exceeding which the process is terminated (default: `20 min`).
+
+`charliecloud.runOptions`
+: This attribute can be used to provide any extra command line options supported by the `ch-run` command.
+
+`charliecloud.temp`
+: Mounts a path of your choice as the `/tmp` directory in the container. Use the special value `auto` to create a temporary directory each time a container is created.
+
+`charliecloud.registry`
+: The registry from where images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
+
+Read the {ref}`container-charliecloud` page to learn more about how to use Charliecloud containers with Nextflow.
+
+(config-conda)=
+
+## `conda`
+
+The `conda` scope controls the creation of Conda environments by the Conda package manager.
+
+The following settings are available:
+
+`conda.enabled`
+: Enables Conda execution (default: `false`).
+
+`conda.cacheDir`
+: Defines the path where Conda environments are stored. Ensure the path is accessible from all compute nodes when using a shared file system.
+
+`conda.channels`
+: Defines the Conda channels that can be used to resolve Conda packages. Channels can be defined as a list (e.g., `['bioconda','conda-forge']`) or a comma separated list string (e.g., `'bioconda,conda-forge'`). Channel priority decreases from left to right.
+
+`conda.createOptions`
+: Defines extra command line options supported by the `conda create` command. See the [Conda documentation](https://docs.conda.io/projects/conda/en/latest/commands/create.html) for more information.
+
+`conda.createTimeout`
+: Defines the amount of time the Conda environment creation can last. The creation process is terminated when the timeout is exceeded (default: `20 min`).
+
+`conda.useMamba`
+: Uses the `mamba` binary instead of `conda` to create the Conda environments. See the [Mamba documentation](https://github.com/mamba-org/mamba) for more information about Mamba.
+
+`conda.useMicromamba`
+: :::{versionadded} 22.05.0-edge
+  :::
+: Uses the `micromamba` binary instead of `conda` to create Conda environments. See the [Micromamba documentation](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html) for more information about Micromamba.
+
+See {ref}`conda-page` for more information about using Conda environments with Nextflow.
+
+(config-dag)=
+
+## `dag`
+
+The `dag` scope controls the workflow diagram generated by Nextflow.
+
+The following settings are available:
+
+`dag.enabled`
+: When `true` enables the generation of the DAG file (default: `false`).
+
+`dag.depth`
+: :::{versionadded} 23.10.0
+  :::
+: *Only supported by the HTML and Mermaid renderers.*
+: Controls the maximum depth at which to render sub-workflows (default: no limit).
+
+`dag.direction`
+: :::{versionadded} 23.10.0
+  :::
+: *Only supported by the HTML and Mermaid renderers.*
+: Controls the direction of the DAG, can be `'LR'` (left-to-right) or `'TB'` (top-to-bottom) (default: `'TB'`).
+
+`dag.file`
+: Graph file name (default: `dag-<timestamp>.html`).
+
+`dag.overwrite`
+: When `true` overwrites any existing DAG file with the same name (default: `false`).
+
+`dag.verbose`
+: :::{versionadded} 23.10.0
+  :::
+: *Only supported by the HTML and Mermaid renderers.*
+: When `false`, channel names are omitted, operators are collapsed, and empty workflow inputs are removed (default: `false`).
+
+Read the {ref}`workflow-diagram` page to learn more about the workflow graph that can be generated by Nextflow.
+
+(config-docker)=
+
+## `docker`
+
+The `docker` scope controls how [Docker](https://www.docker.com) containers are executed by Nextflow.
+
+The following settings are available:
+
+`docker.enabled`
+: Enable Docker execution (default: `false`).
+
+`docker.engineOptions`
+: This attribute can be used to provide any option supported by the Docker engine i.e. `docker [OPTIONS]`.
+
+`docker.envWhitelist`
+: Comma separated list of environment variable names to be included in the container environment.
+
+`docker.fixOwnership`
+: Fix ownership of files created by the docker container.
+
+`docker.legacy`
+: Use command line options removed since Docker 1.10.0 (default: `false`).
+
+`docker.mountFlags`
+: Add the specified flags to the volume mounts e.g. `mountFlags = 'ro,Z'`.
+
+`docker.registry`
+: The registry from where Docker images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
+
+`docker.remove`
+: Clean-up the container after the execution (default: `true`). See the [Docker documentation](https://docs.docker.com/engine/reference/run/#clean-up---rm) for details.
+
+`docker.runOptions`
+: This attribute can be used to provide any extra command line options supported by the `docker run` command. See the [Docker documentation](https://docs.docker.com/engine/reference/run/) for details.
+
+`docker.sudo`
+: Executes Docker run command as `sudo` (default: `false`).
+
+`docker.temp`
+: Mounts a path of your choice as the `/tmp` directory in the container. Use the special value `auto` to create a temporary directory each time a container is created.
+
+`docker.tty`
+: Allocates a pseudo-tty (default: `false`).
+
+Read the {ref}`container-docker` page to learn more about how to use Docker containers with Nextflow.
+
+(config-env)=
+
+## `env`
+
+The `env` scope allows the definition one or more variables that will be exported into the environment where workflow tasks are executed.
+
+Simply prefix your variable names with the `env` scope or surround them by curly brackets, as shown below:
+
+```groovy
+env.ALPHA = 'some value'
+env.BETA = "$HOME/some/path"
+
+env {
+     DELTA = 'one more'
+     GAMMA = "/my/path:$PATH"
+}
+```
+
+:::{note}
+In the above example, variables like `$HOME` and `$PATH` are evaluated when the workflow is launched. If you want these variables to be evaluated during task execution, escape them with `\$`. This difference is important for variables like `$PATH`, which may be different in the workflow environment versus the task environment.
+:::
+
+:::{warning}
+The `env` scope provides environment variables to *tasks*, not Nextflow itself. Nextflow environment variables such as `NXF_VER` should be set in the environment in which Nextflow is launched.
+:::
+
+(config-executor)=
+
+## `executor`
+
+The `executor` scope controls various executor behaviors.
+
+The following settings are available:
+
+`executor.account`
+: :::{versionadded} 24.04.0
+  :::
+: *Used only by the {ref}`slurm-executor`, {ref}`lsf-executor`, {ref}`pbs-executor` and {ref}`pbspro-executor` executors.*
+: Allows specifying the project or organization account that should be charged for running the pipeline jobs.
+
+`executor.cpus`
+: The maximum number of CPUs made available by the underlying system. Used only by the `local` executor.
+
+`executor.dumpInterval`
+: Determines how often to log the executor status (default: `5min`).
+
+`executor.exitReadTimeout`
+: Determines how long to wait before returning an error status when a process is terminated but the `.exitcode` file does not exist or is empty (default: `270 sec`). Used only by grid executors.
+
+`executor.jobName`
+: Determines the name of jobs submitted to the underlying cluster executor e.g. `executor.jobName = { "$task.name - $task.hash" }`. Make sure the resulting job name matches the validation constraints of the underlying batch scheduler.
+: This setting is supported by the following executors: Bridge, Condor, Flux, HyperQueue, Lsf, Moab, Nqsii, Oar, PBS, PBS Pro, SGE, SLURM and Google Batch.
+
+`executor.killBatchSize`
+: Determines the number of jobs that can be killed in a single command execution (default: `100`).
+
+`executor.memory`
+: The maximum amount of memory made available by the underlying system. Used only by the `local` executor.
+
+`executor.name`
+: The name of the executor to be used (default: `local`).
+
+`executor.perCpuMemAllocation`
+: :::{versionadded} 23.07.0-edge
+  :::
+: *Used only by the {ref}`slurm-executor` executor.*
+: When `true`, specifies memory allocations for SLURM jobs as `--mem-per-cpu <task.memory / task.cpus>` instead of `--mem <task.memory>`.
+
+`executor.perJobMemLimit`
+: Specifies Platform LSF *per-job* memory limit mode. See {ref}`lsf-executor`.
+
+`executor.perTaskReserve`
+: Specifies Platform LSF *per-task* memory reserve mode. See {ref}`lsf-executor`.
+
+`executor.pollInterval`
+: Determines how often to check for process termination. Default varies for each executor (see below).
+
+`executor.queueGlobalStatus`
+: :::{versionadded} 23.01.0-edge
+  :::
+: Determines how job status is retrieved. When `false` only the queue associated with the job execution is queried. When `true` the job status is queried globally i.e. irrespective of the submission queue (default: `false`).
+
+`executor.queueSize`
+: The number of tasks the executor will handle in a parallel manner. A queue size of zero corresponds to no limit. Default varies for each executor (see below).
+
+`executor.queueStatInterval`
+: Determines how often to fetch the queue status from the scheduler (default: `1min`). Used only by grid executors.
+
+`executor.retry.delay`
+: :::{versionadded} 22.03.0-edge
+  :::
+: Delay when retrying failed job submissions (default: `500ms`). Used only by grid executors.
+
+`executor.retry.jitter`
+: :::{versionadded} 22.03.0-edge
+  :::
+: Jitter value when retrying failed job submissions (default: `0.25`). Used only by grid executors.
+
+`executor.retry.maxAttempt`
+: :::{versionadded} 22.03.0-edge
+  :::
+: Max attempts when retrying failed job submissions (default: `3`). Used only by grid executors.
+
+`executor.retry.maxDelay`
+: :::{versionadded} 22.03.0-edge
+  :::
+: Max delay when retrying failed job submissions (default: `30s`). Used only by grid executors.
+
+`executor.retry.reason`
+: :::{versionadded} 22.03.0-edge
+  :::
+: Regex pattern that when verified cause a failed submit operation to be re-tried (default: `Socket timed out`). Used only by grid executors.
+
+`executor.submitRateLimit`
+: Determines the max rate of job submission per time unit, for example `'10sec'` (10 jobs per second) or `'50/2min'` (50 jobs every 2 minutes) (default: unlimited).
+
+Some executor settings have different default values depending on the executor.
+
+| Executor       | `queueSize` | `pollInterval` |
+| -------------- | ----------- | -------------- |
+| AWS Batch      | `1000`      | `10s`          |
+| Azure Batch    | `1000`      | `10s`          |
+| Google Batch   | `1000`      | `10s`          |
+| Grid Executors | `100`       | `5s`           |
+| Kubernetes     | `100`       | `5s`           |
+| Local          | N/A         | `100ms`        |
+
+The executor settings can be defined as shown below:
+
+```groovy
+executor {
+    name = 'sge'
+    queueSize = 200
+    pollInterval = '30 sec'
+}
+```
+
+When using two (or more) different executors in your pipeline, you can specify their settings separately by prefixing the executor name with the symbol `$` and using it as special scope identifier. For example:
+
+```groovy
+executor {
+  $sge {
+      queueSize = 100
+      pollInterval = '30sec'
+  }
+
+  $local {
+      cpus = 8
+      memory = '32 GB'
+  }
+}
+```
+
+The above configuration example can be rewritten using the dot notation as shown below:
+
+```groovy
+executor.$sge.queueSize = 100
+executor.$sge.pollInterval = '30sec'
+executor.$local.cpus = 8
+executor.$local.memory = '32 GB'
+```
+
+(config-fusion)=
+
+## `fusion`
+
+The `fusion` scope provides advanced configuration for the use of the {ref}`Fusion file system <fusion-page>`.
+
+The following settings are available:
+
+`fusion.enabled`
+: Enable/disable the use of Fusion file system.
+
+`fusion.cacheSize`
+: :::{versionadded} 23.11.0-edge
+  :::
+: The maximum size of the local cache used by the Fusion client.
+
+`fusion.containerConfigUrl`
+: The URL from where the container layer provisioning the Fusion client is downloaded. This option is useful to specify a development Fusion version for debugging purposes. 
+
+`fusion.exportStorageCredentials`
+: :::{versionadded} 23.05.0-edge
+  This option was previously named `fusion.exportAwsAccessKeys`.
+  :::
+: When `true` the access credentials required by the underlying object storage are exported to the task execution environment.
+
+`fusion.logLevel`
+: The level of logging emitted by the Fusion client.
+
+`fusion.logOutput`
+: Where the logging output is written. 
+
+`fusion.privileged`
+: :::{versionadded} 23.10.0
+  :::
+: Enables the use of privileged containers when using Fusion (default: `true`).
+: The use of Fusion without privileged containers is currently only supported for Kubernetes, and it requires the [k8s-fuse-plugin](https://github.com/nextflow-io/k8s-fuse-plugin) (or similar FUSE device plugin) to be installed in the cluster.
+
+`fusion.tags`
+: The pattern that determines how tags are applied to files created via the Fusion client (default: `[.command.*|.exitcode|.fusion.*](nextflow.io/metadata=true),[*](nextflow.io/temporary=true)`).
+: To disable tags set it to `false`.
+
+(config-google)=
+
+## `google`
+
+The `google` scope allows you to configure the interactions with Google Cloud, including Google Cloud Batch, Google Life Sciences, and Google Cloud Storage.
+
+Read the {ref}`google-page` page for more information.
+
+### Cloud Batch
+
+The following settings are available for Google Cloud Batch:
+
+`google.enableRequesterPaysBuckets`
+: When `true` uses the given Google Cloud project ID as the billing project for storage access. This is required when accessing data from *requester pays enabled* buckets. See [Requester Pays on Google Cloud Storage documentation](https://cloud.google.com/storage/docs/requester-pays) (default: `false`).
+
+`google.httpConnectTimeout`
+: :::{versionadded} 23.06.0-edge
+  :::
+: Defines the HTTP connection timeout for Cloud Storage API requests (default: `'60s'`).
+
+`google.httpReadTimeout`
+: :::{versionadded} 23.06.0-edge
+  :::
+: Defines the HTTP read timeout for Cloud Storage API requests (default: `'60s'`).
+
+`google.location`
+: The Google Cloud location where jobs are executed (default: `us-central1`).
+
+`google.project`
+: The Google Cloud project ID to use for pipeline execution
+
+`google.batch.allowedLocations`
+: :::{versionadded} 22.12.0-edge
+  :::
+: Define the set of allowed locations for VMs to be provisioned. See [Google documentation](https://cloud.google.com/batch/docs/reference/rest/v1/projects.locations.jobs#locationpolicy) for details (default: no restriction).
+
+`google.batch.autoRetryExitCodes`
+: :::{versionadded} 24.07.0-edge
+  :::
+: Defines the list of exit codes that will be automatically retried by Google Batch when `google.batch.maxSpotAttempts` is greater than 0 (default `[50001]`). Refer to the [Google Batch documentation](https://cloud.google.com/batch/docs/troubleshooting#reserved-exit-codes) for the list of retryable exit codes.
+
+`google.batch.bootDiskImage`
+: :::{versionadded} 24.08.0-edge
+  :::
+: Set the image URI of the virtual machine boot disk, e.g `batch-debian`. See [Google documentation](https://cloud.google.com/batch/docs/vm-os-environment-overview#vm-os-image-options) for details (default: none).
+
+`google.batch.bootDiskSize`
+: Set the size of the virtual machine boot disk, e.g `50.GB` (default: none).
+
+`google.batch.cpuPlatform`
+: Set the minimum CPU Platform, e.g. `'Intel Skylake'`. See [Specifying a minimum CPU Platform for VM instances](https://cloud.google.com/compute/docs/instances/specify-min-cpu-platform#specifications) (default: none).
+
+`google.batch.maxSpotAttempts`
+: :::{versionadded} 23.11.0-edge
+  :::
+: :::{versionchanged} 24.08.0-edge
+  The default value was changed from `5` to `0`.
+  :::
+: Max number of execution attempts of a job interrupted by a Compute Engine spot reclaim event (default: `0`).
+: See also: `google.batch.autoRetryExitCodes`
+
+`google.batch.network`
+: The URL of an existing network resource to which the VM will be attached.
+
+  You can specify the network as a full or partial URL. For example, the following are all valid URLs:
+
+  - https://www.googleapis.com/compute/v1/projects/{project}/global/networks/{network}
+  - projects/{project}/global/networks/{network}
+  - global/networks/{network}
+
+`google.batch.serviceAccountEmail`
+: Define the Google service account email to use for the pipeline execution. If not specified, the default Compute Engine service account for the project will be used.
+
+: Note that the `google.batch.serviceAccountEmail` service account will only be used for spawned jobs, not for the Nextflow process itself.  See the [Google Cloud](https://www.nextflow.io/docs/latest/google.html#credentials) documentation for more information on credentials.
+
+`google.batch.spot`
+: When `true` enables the usage of *spot* virtual machines or `false` otherwise (default: `false`).
+
+`google.batch.subnetwork`
+: The URL of an existing subnetwork resource in the network to which the VM will be attached.
+
+  You can specify the subnetwork as a full or partial URL. For example, the following are all valid URLs:
+
+  - https://www.googleapis.com/compute/v1/projects/{project}/regions/{region}/subnetworks/{subnetwork}
+  - projects/{project}/regions/{region}/subnetworks/{subnetwork}
+  - regions/{region}/subnetworks/{subnetwork}
+
+`google.batch.usePrivateAddress`
+: When `true` the VM will NOT be provided with a public IP address, and only contain an internal IP. If this option is enabled, the associated job can only load docker images from Google Container Registry, and the job executable cannot use external services other than Google APIs (default: `false`).
+
+`google.storage.maxAttempts`
+: :::{versionadded} 23.11.0-edge
+  :::
+: Max attempts when retrying failed API requests to Cloud Storage (default: `10`).
+
+`google.storage.maxDelay`
+: :::{versionadded} 23.11.0-edge
+  :::
+: Max delay when retrying failed API requests to Cloud Storage (default: `'90s'`).
+
+`google.storage.multiplier`
+: :::{versionadded} 23.11.0-edge
+  :::
+: Delay multiplier when retrying failed API requests to Cloud Storage (default: `2.0`).
+
+### Cloud Life Sciences
+
+The following settings are available for Cloud Life Sciences:
+
+`google.enableRequesterPaysBuckets`
+: When `true` uses the given Google Cloud project ID as the billing project for storage access. This is required when accessing data from *requester pays enabled* buckets. See [Requester Pays on Google Cloud Storage documentation](https://cloud.google.com/storage/docs/requester-pays) (default: `false`).
+
+`google.httpConnectTimeout`
+: :::{versionadded} 23.06.0-edge
+  :::
+: Defines the HTTP connection timeout for Cloud Storage API requests (default: `'60s'`).
+
+`google.httpReadTimeout`
+: :::{versionadded} 23.06.0-edge
+  :::
+: Defines the HTTP read timeout for Cloud Storage API requests (default: `'60s'`).
+
+`google.location`
+: The Google Cloud location where jobs are executed (default: `us-central1`).
+
+`google.project`
+: The Google Cloud project ID to use for pipeline execution
+
+`google.region`
+: The Google Cloud region where jobs are executed. Multiple regions can be provided as a comma-separated list. Cannot be used with the `google.zone` option. See the [Google Cloud documentation](https://cloud.google.com/compute/docs/regions-zones/) for a list of available regions and zones.
+
+`google.zone`
+: The Google Cloud zone where jobs are executed. Multiple zones can be provided as a comma-separated list. Cannot be used with the `google.region` option. See the [Google Cloud documentation](https://cloud.google.com/compute/docs/regions-zones/) for a list of available regions and zones.
+
+`google.lifeSciences.bootDiskSize`
+: Set the size of the virtual machine boot disk e.g `50.GB` (default: none).
+
+`google.lifeSciences.copyImage`
+: The container image run to copy input and output files. It must include the `gsutil` tool (default: `google/cloud-sdk:alpine`).
+
+`google.lifeSciences.cpuPlatform`
+: Set the minimum CPU Platform e.g. `'Intel Skylake'`. See [Specifying a minimum CPU Platform for VM instances](https://cloud.google.com/compute/docs/instances/specify-min-cpu-platform#specifications) (default: none).
+
+`google.lifeSciences.debug`
+: When `true` copies the `/google` debug directory in that task bucket directory (default: `false`).
+
+`google.lifeSciences.keepAliveOnFailure`
+: :::{versionadded} 21.06.0-edge
+  :::
+: When `true` and a task complete with an unexpected exit status the associated compute node is kept up for 1 hour. This options implies `sshDaemon=true` (default: `false`).
+
+`google.lifeSciences.network`
+: :::{versionadded} 21.03.0-edge
+  :::
+: Set network name to attach the VM's network interface to. The value will be prefixed with `global/networks/` unless it contains a `/`, in which case it is assumed to be a fully specified network resource URL. If unspecified, the global default network is used.
+
+`google.lifeSciences.preemptible`
+: When `true` enables the usage of *preemptible* virtual machines or `false` otherwise (default: `true`).
+
+`google.lifeSciences.serviceAccountEmail`
+: :::{versionadded} 20.05.0-edge
+  :::
+: Define the Google service account email to use for the pipeline execution. If not specified, the default Compute Engine service account for the project will be used.
+
+`google.lifeSciences.subnetwork`
+: :::{versionadded} 21.03.0-edge
+  :::
+: Define the name of the subnetwork to attach the instance to must be specified here, when the specified network is configured for custom subnet creation. The value is prefixed with `regions/subnetworks/` unless it contains a `/`, in which case it is assumed to be a fully specified subnetwork resource URL.
+
+`google.lifeSciences.sshDaemon`
+: When `true` runs SSH daemon in the VM carrying out the job to which it's possible to connect for debugging purposes (default: `false`).
+
+`google.lifeSciences.sshImage`
+: The container image used to run the SSH daemon (default: `gcr.io/cloud-genomics-pipelines/tools`).
+
+`google.lifeSciences.usePrivateAddress`
+: :::{versionadded} 20.03.0-edge
+  :::
+: When `true` the VM will NOT be provided with a public IP address, and only contain an internal IP. If this option is enabled, the associated job can only load docker images from Google Container Registry, and the job executable cannot use external services other than Google APIs (default: `false`).
+
+`google.storage.delayBetweenAttempts`
+: :::{versionadded} 21.06.0-edge
+  :::
+: Delay between download attempts from Google Storage (default `10 sec`).
+
+`google.storage.downloadMaxComponents`
+: :::{versionadded} 21.06.0-edge
+  :::
+: Defines the value for the option `GSUtil:sliced_object_download_max_components` used by `gsutil` for transfer input and output data (default: `8`).
+
+`google.storage.maxParallelTransfers`
+: :::{versionadded} 21.06.0-edge
+  :::
+: Max parallel upload/download transfer operations *per job* (default: `4`).
+
+`google.storage.maxTransferAttempts`
+: :::{versionadded} 21.06.0-edge
+  :::
+: Max number of downloads attempts from Google Storage (default: `1`).
+
+`google.storage.parallelThreadCount`
+: :::{versionadded} 21.06.0-edge
+  :::
+: Defines the value for the option `GSUtil:parallel_thread_count` used by `gsutil` for transfer input and output data (default: `1`).
+
+(config-k8s)=
+
+## `k8s`
+
+The `k8s` scope controls the deployment and execution of workflow applications in a Kubernetes cluster.
+
+The following settings are available:
+
+`k8s.autoMountHostPaths`
+: Automatically mounts host paths into the task pods (default: `false`). Only intended for development purposes when using a single node.
+
+`k8s.computeResourceType`
+: :::{versionadded} 22.05.0-edge
+  :::
+: Define whether use Kubernetes `Pod` or `Job` resource type to carry out Nextflow tasks (default: `Pod`).
+
+`k8s.context`
+: Defines the Kubernetes [configuration context name](https://kubernetes.io/docs/tasks/access-application-cluster/configure-access-multiple-clusters/) to use.
+
+`k8s.cpuLimits`
+: :::{versionadded} 24.04.0
+  :::
+: When `true`, set both the pod CPUs `request` and `limit` to the value specified by the `cpus` directive, otherwise set only the `request` (default: `false`).
+: This setting is useful when a K8s cluster requires a CPU limit to be defined through a [LimitRange](https://kubernetes.io/docs/concepts/policy/limit-range/).
+
+`k8s.debug.yaml`
+: When `true`, saves the pod spec for each task to `.command.yaml` in the task directory (default: `false`).
+
+`k8s.fetchNodeName`
+: :::{versionadded} 22.05.0-edge
+  :::
+: If you trace the hostname, activate this option (default: `false`).
+
+`k8s.fuseDevicePlugin`
+: :::{versionadded} 24.01.0-edge
+  :::
+: The FUSE device plugin to be used when enabling Fusion in unprivileged mode (default: `['nextflow.io/fuse': 1]`).
+
+`k8s.httpConnectTimeout`
+: :::{versionadded} 22.10.0
+  :::
+: Defines the Kubernetes client request HTTP connection timeout e.g. `'60s'`.
+
+`k8s.httpReadTimeout`
+: :::{versionadded} 22.10.0
+  :::
+: Defines the Kubernetes client request HTTP connection read timeout e.g. `'60s'`.
+
+`k8s.launchDir`
+: Defines the path where the workflow is launched and the user data is stored. This must be a path in a shared K8s persistent volume (default: `<volume-claim-mount-path>/<user-name>`).
+
+`k8s.maxErrorRetry`
+: :::{versionadded} 22.09.6-edge
+  :::
+: Defines the Kubernetes API max request retries (default: 4).
+
+`k8s.namespace`
+: Defines the Kubernetes namespace to use (default: `default`).
+
+`k8s.pod`
+: Allows the definition of one or more pod configuration options such as environment variables, config maps, secrets, etc. It allows the same settings as the {ref}`process-pod` process directive.
+: When using the `kuberun` command, this setting also applies to the submitter pod.
+
+`k8s.projectDir`
+: Defines the path where Nextflow projects are downloaded. This must be a path in a shared K8s persistent volume (default: `<volume-claim-mount-path>/projects`).
+
+`k8s.pullPolicy`
+: Defines the strategy to be used to pull the container image e.g. `pullPolicy: 'Always'`.
+
+`k8s.runAsUser`
+: Defines the user ID to be used to run the containers. Shortcut for the `securityContext` option.
+
+`k8s.securityContext`
+: Defines the [security context](https://kubernetes.io/docs/tasks/configure-pod-container/security-context/) for all pods.
+
+`k8s.serviceAccount`
+: Defines the Kubernetes [service account name](https://kubernetes.io/docs/tasks/configure-pod-container/configure-service-account/) to use.
+
+`k8s.storageClaimName`
+: The name of the persistent volume claim where store workflow result data.
+
+`k8s.storageMountPath`
+: The path location used to mount the persistent volume claim (default: `/workspace`).
+
+`k8s.storageSubPath`
+: The path in the persistent volume to be mounted (default: `/`).
+
+`k8s.workDir`
+: Defines the path where the workflow temporary data is stored. This must be a path in a shared K8s persistent volume (default: `<user-dir>/work`).
+
+See the {ref}`k8s-page` page for more details.
+
+(config-mail)=
+
+## `mail`
+
+The `mail` scope controls the mail server used to send email notifications.
+
+The following settings are available:
+
+`mail.debug`
+: When `true` enables Java Mail logging for debugging purpose.
+
+`mail.from`
+: Default email sender address.
+
+`mail.smtp.host`
+: Host name of the mail server.
+
+`mail.smtp.port`
+: Port number of the mail server.
+
+`mail.smtp.user`
+: User name to connect to the mail server.
+
+`mail.smtp.password`
+: User password to connect to the mail server.
+
+`mail.smtp.proxy.host`
+: Host name of an HTTP web proxy server that will be used for connections to the mail server.
+
+`mail.smtp.proxy.port`
+: Port number for the HTTP web proxy server.
+
+`mail.smtp.*`
+: Any SMTP configuration property supported by the [Java Mail API](https://javaee.github.io/javamail/), which Nextflow uses to send emails. See the table of available properties [here](https://javaee.github.io/javamail/docs/api/com/sun/mail/smtp/package-summary.html#properties).
+
+For example, the following snippet shows how to configure Nextflow to send emails through the [AWS Simple Email Service](https://aws.amazon.com/ses/):
+
+```groovy
+mail {
+    smtp.host = 'email-smtp.us-east-1.amazonaws.com'
+    smtp.port = 587
+    smtp.user = '<Your AWS SES access key>'
+    smtp.password = '<Your AWS SES secret key>'
+    smtp.auth = true
+    smtp.starttls.enable = true
+    smtp.starttls.required = true
+}
+```
+
+:::{note}
+Some versions of Java (e.g. Java 11 Corretto) do not default to TLS v1.2, and as a result may have issues with 3rd party integrations that enforce TLS v1.2 (e.g. Azure Active Directory OIDC). This problem can be addressed by setting the following config option:
+
+```groovy
+mail {
+    smtp.ssl.protocols = 'TLSv1.2'
+}
+```
+:::
+
+(config-manifest)=
+
+## `manifest`
+
+The `manifest` scope allows you to define some meta-data information needed when publishing or running your pipeline.
+
+The following settings are available:
+
+`manifest.author`
+: :::{deprecated} 24.09.0-edge
+  Use `manifest.contributors` instead.
+  :::
+: Project author name (use a comma to separate multiple names).
+
+`manifest.contributors`
+: :::{versionadded} 24.09.0-edge
+  :::
+: List of project contributors. Should be a list of maps. The following fields are supported in the contributor map:
+  - `name`: the contributor's name 
+  - `affiliation`: the contributor's affiliated organization
+  - `email`: the contributor's email address
+  - `github`: the contributor's GitHub URL
+  - `contribution`: list of contribution types, each element can be one of `'author'`, `'maintainer'`, or `'contributor'`
+  - `orcid`: the contributor's [ORCID](https://orcid.org/) URL
+
+`manifest.defaultBranch`
+: Git repository default branch (default: `master`).
+
+`manifest.description`
+: Free text describing the workflow project.
+
+`manifest.docsUrl`
+: Project documentation URL.
+
+`manifest.doi`
+: Project related publication DOI identifier.
+
+`manifest.homePage`
+: Project home page URL.
+
+`manifest.icon`
+: Project related icon location (Relative path or URL).
+
+`manifest.license`
+: Project license.
+
+`manifest.mainScript`
+: Project main script (default: `main.nf`).
+
+`manifest.name`
+: Project short name.
+
+`manifest.nextflowVersion`
+: Minimum required Nextflow version.
+
+  This setting may be useful to ensure that a specific version is used:
+
+  ```groovy
+  manifest.nextflowVersion = '1.2.3'        // exact match
+  manifest.nextflowVersion = '1.2+'         // 1.2 or later (excluding 2 and later)
+  manifest.nextflowVersion = '>=1.2'        // 1.2 or later
+  manifest.nextflowVersion = '>=1.2, <=1.5' // any version in the 1.2 .. 1.5 range
+  manifest.nextflowVersion = '!>=1.2'       // with ! prefix, stop execution if current version does not match required version.
+  ```
+
+`manifest.organization`
+: Project organization
+
+`manifest.recurseSubmodules`
+: Pull submodules recursively from the Git repository.
+
+`manifest.version`
+: Project version number.
+
+The above options can also be specified in a `manifest` block, for example:
+
+```groovy
+manifest {
+    homePage = 'http://foo.com'
+    description = 'Pipeline does this and that'
+    mainScript = 'foo.nf'
+    version = '1.0.0'
+}
+```
+
+Read the {ref}`sharing-page` page to learn how to publish your pipeline to GitHub, BitBucket or GitLab.
+
+(config-nextflow)=
+
+## `nextflow`
+
+:::{deprecated} 24.10.0
+The `nextflow.publish` scope has been renamed to `workflow.output`. See {ref}`config-workflow` for more information.
+:::
+
+(config-notification)=
+
+## `notification`
+
+The `notification` scope allows you to define the automatic sending of a notification email message when the workflow execution terminates.
+
+`notification.attributes`
+: A map object modelling the variables that can be used in the template file.
+
+`notification.enabled`
+: Enables the sending of a notification message when the workflow execution completes.
+
+`notification.from`
+: Sender address for the notification email message.
+
+`notification.template`
+: Path of a template file which provides the content of the notification message.
+
+`notification.to`
+: Recipient address for the notification email. Multiple addresses can be specified separating them with a comma.
+
+The notification message is sent my using the STMP server defined in the configuration {ref}`mail scope<config-mail>`.
+
+If no mail configuration is provided, it tries to send the notification message by using the external mail command eventually provided by the underlying system (e.g. `sendmail` or `mail`).
+
+(config-podman)=
+
+## `podman`
+
+The `podman` scope controls how [Podman](https://podman.io/) containers are executed by Nextflow.
+
+The following settings are available:
+
+`podman.enabled`
+: Enable Podman execution (default: `false`).
+
+`podman.engineOptions`
+: This attribute can be used to provide any option supported by the Podman engine i.e. `podman [OPTIONS]`.
+
+`podman.envWhitelist`
+: Comma separated list of environment variable names to be included in the container environment.
+
+`podman.mountFlags`
+: Add the specified flags to the volume mounts e.g. `mountFlags = 'ro,Z'`.
+
+`podman.registry`
+: The registry from where container images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
+
+`podman.remove`
+: Clean-up the container after the execution (default: `true`).
+
+`podman.runOptions`
+: This attribute can be used to provide any extra command line options supported by the `podman run` command.
+
+`podman.temp`
+: Mounts a path of your choice as the `/tmp` directory in the container. Use the special value `auto` to create a temporary directory each time a container is created.
+
+Read the {ref}`container-podman` page to learn more about how to use Podman containers with Nextflow.
+
+(config-report)=
+
+## `report`
+
+The `report` scope allows you to configure the workflow {ref}`execution-report`.
+
+The following settings are available:
+
+`report.enabled`
+: If `true` it create the workflow execution report.
+
+`report.file`
+: The path of the created execution report file (default: `report-<timestamp>.html`).
+
+`report.overwrite`
+: When `true` overwrites any existing report file with the same name.
+
+(config-sarus)=
+
+## `sarus`
+
+The ``sarus`` scope controls how [Sarus](https://sarus.readthedocs.io) containers are executed by Nextflow.
+
+The following settings are available:
+
+`sarus.enabled`
+: Enable Sarus execution (default: `false`).
+
+`sarus.envWhitelist`
+: Comma separated list of environment variable names to be included in the container environment.
+
+`sarus.runOptions`
+: This attribute can be used to provide any extra command line options supported by the `sarus run` command. For details see the [Sarus user guide](https://sarus.readthedocs.io/en/stable/user/user_guide.html).
+
+`sarus.tty`
+: Allocates a pseudo-tty (default: `false`).
+
+Read the {ref}`container-sarus` page to learn more about how to use Sarus containers with Nextflow.
+
+(config-shifter)=
+
+## `shifter`
+
+The `shifter` scope controls how [Shifter](https://docs.nersc.gov/programming/shifter/overview/) containers are executed by Nextflow.
+
+The following settings are available:
+
+`shifter.enabled`
+: Enable Shifter execution (default: `false`).
+
+Read the {ref}`container-shifter` page to learn more about how to use Shifter containers with Nextflow.
+
+(config-singularity)=
+
+## `singularity`
+
+The `singularity` scope controls how [Singularity](https://sylabs.io/singularity/) containers are executed by Nextflow.
+
+The following settings are available:
+
+`singularity.autoMounts`
+: When `true` Nextflow automatically mounts host paths in the executed container. It requires the `user bind control` feature to be enabled in your Singularity installation (default: `true`).
+: :::{versionchanged} 23.09.0-edge
+  Default value was changed from `false` to `true`.
+  :::
+
+`singularity.cacheDir`
+: The directory where remote Singularity images are stored. When using a computing cluster it must be a shared folder accessible to all compute nodes.
+
+`singularity.enabled`
+: Enable Singularity execution (default: `false`).
+
+`singularity.engineOptions`
+: This attribute can be used to provide any option supported by the Singularity engine i.e. `singularity [OPTIONS]`.
+
+`singularity.envWhitelist`
+: Comma separated list of environment variable names to be included in the container environment.
+
+`singularity.libraryDir`
+: Directory where remote Singularity images are retrieved. When using a computing cluster it must be a shared folder accessible to all compute nodes.
+
+`singularity.noHttps`
+: Pull the Singularity image with http protocol (default: `false`).
+
+`singularity.ociAutoPull`
+: :::{versionadded} 23.12.0-edge
+  :::
+: When enabled, OCI (and Docker) container images are pull and converted to a SIF image file format implicitly by the Singularity run command, instead of Nextflow. Requires Singularity 3.11 or later (default: `false`).
+
+  :::{note}
+  Leave `ociAutoPull` disabled if willing to build a Singularity native image with Wave (see the {ref}`wave-singularity` section).
+  :::
+
+`singularity.ociMode`
+: :::{versionadded} 23.12.0-edge
+  :::
+: Enable OCI-mode, that allows running native OCI compliant container image with Singularity using `crun` or `runc` as low-level runtime. Note: it requires Singularity 4 or later. See `--oci` flag in the [Singularity documentation](https://docs.sylabs.io/guides/4.0/user-guide/oci_runtime.html#oci-mode) for more details and requirements (default: `false`).
+
+  :::{note}
+  Leave `ociMode` disabled if you are willing to build a Singularity native image with Wave (see the {ref}`wave-singularity` section).
+  :::
+
+`singularity.pullTimeout`
+: The amount of time the Singularity pull can last, exceeding which the process is terminated (default: `20 min`).
+
+`singularity.registry`
+: :::{versionadded} 22.12.0-edge
+  :::
+: The registry from where Docker images are pulled. It should be only used to specify a private registry server. It should NOT include the protocol prefix i.e. `http://`.
+
+`singularity.runOptions`
+: This attribute can be used to provide any extra command line options supported by `singularity exec`.
+
+Read the {ref}`container-singularity` page to learn more about how to use Singularity containers with Nextflow.
+
+(config-spack)=
+
+## `spack`
+
+The `spack` scope controls the creation of a Spack environment by the Spack package manager.
+
+The following settings are available:
+
+`spack.cacheDir`
+: Defines the path where Spack environments are stored. When using a compute cluster make sure to provide a shared file system path accessible from all compute nodes.
+
+`spack.checksum`
+: Enables checksum verification for source tarballs (default: `true`). Only disable when requesting a package version not yet encoded in the corresponding Spack recipe.
+
+`spack.createTimeout`
+: Defines the amount of time the Spack environment creation can last. The creation process is terminated when the timeout is exceeded (default: `60 min`).
+
+`spack.parallelBuilds`
+: Sets number of parallel package builds (Spack default: coincides with number of available CPU cores).
+
+Nextflow does not allow for fine-grained configuration of the Spack package manager. Instead, this has to be performed directly on the host Spack installation. For more information see the [Spack documentation](https://spack.readthedocs.io).
+
+(config-timeline)=
+
+## `timeline`
+
+The `timeline` scope controls the execution timeline report generated by Nextflow.
+
+The following settings are available:
+
+`timeline.enabled`
+: When `true` enables the generation of the timeline report file (default: `false`).
+
+`timeline.file`
+: Timeline file name (default: `timeline-<timestamp>.html`).
+
+`timeline.overwrite`
+: When `true` overwrites any existing timeline file with the same name.
+
+(config-tower)=
+
+## `tower`
+
+The `tower` scope controls the settings for the [Seqera Platform](https://seqera.io) (formerly Tower Cloud).
+
+The following settings are available:
+
+`tower.accessToken`
+: The unique access token specific to your account on an instance of Seqera Platform.
+
+  Your `accessToken` can be obtained from your Seqera Platform instance in the [Tokens page](https://cloud.seqera.io/tokens).
+
+`tower.enabled`
+: When `true` Nextflow sends the workflow tracing and execution metrics to Seqera Platform (default: `false`).
+
+`tower.endpoint`
+: The endpoint of your Seqera Platform instance (default: `https://api.cloud.seqera.io`).
+
+`tower.workspaceId`
+: The ID of the Seqera Platform workspace where the run should be added (default: the launching user personal workspace).
+
+  The workspace ID can also be specified using the environment variable `TOWER_WORKSPACE_ID` (config file has priority over the environment variable).
+
+(config-trace)=
+
+## `trace`
+
+The `trace` scope controls the layout of the execution trace file generated by Nextflow.
+
+The following settings are available:
+
+`trace.enabled`
+: When `true` turns on the generation of the execution trace report file (default: `false`).
+
+`trace.fields`
+: Comma separated list of fields to be included in the report. The available fields are listed at {ref}`this page <trace-fields>`.
+
+`trace.file`
+: Trace file name (default: `trace-<timestamp>.txt`).
+
+`trace.overwrite`
+: When `true` overwrites any existing trace file with the same name.
+
+`trace.raw`
+: When `true` turns on raw number report generation i.e. date and time are reported as milliseconds and memory as number of bytes.
+
+`trace.sep`
+: Character used to separate values in each row (default: `\t`).
+
+The above options can also be specified in a `trace` block, for example:
+
+```groovy
+trace {
+    enabled = true
+    file = 'pipeline_trace.txt'
+    fields = 'task_id,name,status,exit,realtime,%cpu,rss'
+}
+```
+
+Read the {ref}`trace-report` page to learn more about the execution report that can be generated by Nextflow.
+
+(config-wave)=
+
+## `wave`
+
+The `wave` scope provides advanced configuration for the use of {ref}`Wave containers <wave-page>`.
+
+The following settings are available:
+
+`wave.enabled`
+: Enable/disable the use of Wave containers.
+
+`wave.build.repository`
+: The container repository where images built by Wave are uploaded (note: the corresponding credentials must be provided in your Seqera Platform account).
+
+`wave.build.cacheRepository`
+: The container repository used to cache image layers built by the Wave service (note: the corresponding credentials must be provided in your Seqera Platform account).
+
+`wave.build.conda.basePackages`
+: One or more Conda packages to be always added in the resulting container (default: `conda-forge::procps-ng`).
+
+`wave.build.conda.commands`
+: One or more commands to be added to the Dockerfile used to build a Conda based image.
+
+`wave.build.conda.mambaImage`
+: The Mamba container image is used to build Conda based container. This is expected to be [micromamba-docker](https://github.com/mamba-org/micromamba-docker) image.
+
+`wave.build.spack.basePackages`
+: :::{versionadded} 22.06.0-edge
+  :::
+: One or more Spack packages to be always added in the resulting container.
+
+`wave.build.spack.commands`
+: :::{versionadded} 22.06.0-edge
+  :::
+: One or more commands to be added to the Dockerfile used to build a Spack based image.
+
+`wave.endpoint`
+: The Wave service endpoint (default: `https://wave.seqera.io`).
+
+`wave.freeze`
+: :::{versionadded} 23.07.0-edge
+  :::
+: Enables Wave container freezing. Wave will provision a non-ephemeral container image that will be pushed to a container repository of your choice. It requires the use of the `wave.build.repository` setting.
+: It is also recommended to specify a custom cache repository using `wave.build.cacheRepository`.
+: :::{note}
+  The container repository authentication must be managed by the underlying infrastructure.
+  :::
+
+`wave.httpClient.connectTime`
+: :::{versionadded} 22.06.0-edge
+  :::
+: Sets the connection timeout duration for the HTTP client connecting to the Wave service (default: `30s`).
+
+`wave.mirror`
+: :::{versionadded} 24.09.1-edge
+  :::
+: Enables Wave container mirroring.
+: This feature allow mirroring (i.e. copying) the containers defined in your pipeline
+  configuration to a container registry of your choice, so that pipeline tasks will pull the copied containers from the
+  target registry instead of the original one.
+: The resulting copied containers will maintain the name, digest and metadata.
+: The target registry is expected to be specified by using the `wave.build.repository` option.
+: :::{note}
+  * This feature is only compatible with `wave.strategy = 'container'` option.
+  * This feature cannot be used with Wave *freeze* mode.
+  * The authentication of the resulting container images must be managed by the underlying infrastructure.
+  :::
+
+`wave.retryPolicy.delay`
+: :::{versionadded} 22.06.0-edge
+  :::
+: The initial delay when a failing HTTP request is retried (default: `150ms`).
+
+`wave.retryPolicy.jitter`
+: :::{versionadded} 22.06.0-edge
+  :::
+: The jitter factor used to randomly vary retry delays (default: `0.25`).
+
+`wave.retryPolicy.maxAttempts`
+: :::{versionadded} 22.06.0-edge
+  :::
+: The max number of attempts a failing HTTP request is retried (default: `5`).
+
+`wave.retryPolicy.maxDelay`
+: :::{versionadded} 22.06.0-edge
+  :::
+: The max delay when a failing HTTP request is retried (default: `90 seconds`).
+
+`wave.scan.mode`
+: :::{versionadded} 24.09.1-edge
+  :::
+: Determines the container security scanning execution modality.
+
+: This feature allows scanning for security vulnerability the container used in your pipeline. The following options can be specified:
+
+  * `none`: No security scan is performed on the containers used by your pipeline.
+  * `async`: The containers used by your pipeline are scanned for security vulnerability. The task execution is carried out independently of the security scan result.
+  * `required`: The containers used by your pipeline are scanned for security vulnerability. The task is only executed if the corresponding container is not affected by a security vulnerability.
+
+`wave.scan.allowedLevels`
+: :::{versionadded} 24.09.1-edge
+  :::
+: Determines the allowed security levels when scanning containers for security vulnerabilities.
+
+: Allowed values are: `low`, `medium`, `high`, `critical`. For example: `wave.scan.allowedLevels = 'low,medium'`.
+
+: This option requires the use of `wave.scan.mode = 'required'`.
+
+`wave.strategy`
+: The strategy to be used when resolving ambiguous Wave container requirements (default: `'container,dockerfile,conda'`).
+
+(config-workflow)=
+
+## `workflow`
+
+:::{versionadded} 24.10.0
+:::
+
+The `workflow` scope provides workflow execution options.
+
+`workflow.failOnIgnore`
+: :::{versionadded} 24.05.0-edge
+  :::
+: When `true`, the pipeline will exit with a non-zero exit code if any failed tasks are ignored using the `ignore` {ref}`error strategy <process-error-strategy>`.
+
+`workflow.onComplete`
+: Specify a closure that will be invoked at the end of a workflow run (including failed runs). See {ref}`workflow-handlers` for more information.
+
+`workflow.onError`
+: Specify a closure that will be invoked if a workflow run is terminated. See {ref}`workflow-handlers` for more information.
+
+`workflow.output.contentType`
+: *Currently only supported for S3.*
+: Specify the media type, also known as [MIME type](https://developer.mozilla.org/en-US/docs/Web/HTTP/MIME_types), of published files (default: `false`). Can be a string (e.g. `'text/html'`), or `true` to infer the content type from the file extension.
+
+`workflow.output.enabled`
+: Enable or disable publishing (default: `true`).
+
+`workflow.output.ignoreErrors`
+: When `true`, the workflow will not fail if a file can't be published for some reason (default: `false`).
+
+`workflow.output.mode`
+: The file publishing method (default: `'symlink'`). The following options are available:
+
+  `'copy'`
+  : Copy each file into the output directory.
+
+  `'copyNoFollow'`
+  : Copy each file into the output directory without following symlinks, i.e. only the link is copied.
+
+  `'link'`
+  : Create a hard link in the output directory for each file.
+
+  `'move'`
+  : Move each file into the output directory.
+  : Should only be used for files which are not used by downstream processes in the workflow.
+
+  `'rellink'`
+  : Create a relative symbolic link in the output directory for each file.
+
+  `'symlink'`
+  : Create an absolute symbolic link in the output directory for each output file.
+
+`workflow.output.overwrite`
+: When `true` any existing file in the specified folder will be overwritten (default: `'standard'`). The following options are available:
+
+  `false`
+  : Never overwrite existing files.
+
+  `true`
+  : Always overwrite existing files.
+
+  `'deep'`
+  : Overwrite existing files when the file content is different.
+
+  `'lenient'`
+  : Overwrite existing files when the file size is different.
+
+  `'standard'`
+  : Overwrite existing files when the file size or last modified timestamp is different.
+
+`workflow.output.retryPolicy.delay`
+: Delay when retrying a failed publish operation (default: `350ms`).
+
+`workflow.output.retryPolicy.jitter`
+: Jitter value when retrying a failed publish operation (default: `0.25`).
+
+`workflow.output.retryPolicy.maxAttempt`
+: Max attempts when retrying a failed publish operation (default: `5`).
+
+`workflow.output.retryPolicy.maxDelay`
+: Max delay when retrying a failed publish operation (default: `90s`).
+
+`workflow.output.storageClass`
+: *Currently only supported for S3.*
+: Specify the storage class for published files.
+
+`workflow.output.tags`
+: *Currently only supported for S3.*
+: Specify arbitrary tags for published files. For example:
+  ```groovy
+  tags FOO: 'hello', BAR: 'world'
+  ```
diff --git a/docs/reference/env-vars.md b/docs/reference/env-vars.md
new file mode 100644
index 0000000000..e9a6f65f6f
--- /dev/null
+++ b/docs/reference/env-vars.md
@@ -0,0 +1,221 @@
+(config-env-vars)=
+
+# Environment variables
+
+The following environment variables control the configuration of the Nextflow runtime and the underlying Java virtual machine.
+
+## Java settings
+
+`JAVA_CMD`
+: Defines the path location of the Java binary command used to launch Nextflow.
+
+`JAVA_HOME`
+: Defines the path location of the Java VM installation used to run Nextflow.
+
+## Nextflow settings
+
+`NXF_ANSI_LOG`
+: Enables/disables ANSI console output (default `true` when ANSI terminal is detected).
+
+`NXF_ANSI_SUMMARY`
+: Enables/disables ANSI completion summary: `true\|false` (default: print summary if execution last more than 1 minute).
+
+`NXF_ASSETS`
+: Defines the directory where downloaded pipeline repositories are stored (default: `$NXF_HOME/assets`)
+
+`NXF_CACHE_DIR`
+: :::{versionadded} 24.02.0-edge
+  :::
+: Defines the base cache directory when using the default cache store (default: `"$launchDir/.nextflow"`).
+
+`NXF_CHARLIECLOUD_CACHEDIR`
+: Directory where remote Charliecloud images are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
+
+`NXF_CLOUDCACHE_PATH`
+: :::{versionadded} 23.07.0-edge
+  :::
+: Defines the base cache path when using the cloud cache store.
+
+`NXF_CLOUD_DRIVER`
+: Defines the default cloud driver to be used if not specified in the config file or as command line option, either `aws` or `google`.
+
+`NXF_CONDA_CACHEDIR`
+: Directory where Conda environments are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
+
+`NXF_CONDA_ENABLED`
+: :::{versionadded} 22.08.0-edge
+  :::
+: Enable the use of Conda recipes defined by using the {ref}`process-conda` directive. (default: `false`).
+
+`NXF_DEFAULT_DSL`
+: :::{versionadded} 22.03.0-edge
+  :::
+: Defines the DSL version that should be used in not specified otherwise in the script of config file (default: `2`)
+
+`NXF_DISABLE_CHECK_LATEST`
+: :::{versionadded} 23.09.0-edge
+  :::
+: Nextflow automatically checks for a newer version of itself unless this option is enabled (default: `false`).
+
+`NXF_DISABLE_JOBS_CANCELLATION`
+: :::{versionadded} 21.12.0-edge
+  :::
+: Disables the cancellation of child jobs on workflow execution termination.
+
+`NXF_DISABLE_PARAMS_TYPE_DETECTION`
+: :::{versionadded} 23.07.0-edge
+  :::
+: Disables the automatic type detection of command line parameters.
+
+`NXF_DISABLE_WAVE_SERVICE`
+: :::{versionadded} 23.08.0-edge
+  :::
+: Disables the requirement for Wave service when enabling the Fusion file system.
+
+`NXF_ENABLE_AWS_SES`
+: :::{versionadded} 23.06.0-edge
+  :::
+: Enable to use of AWS SES native API for sending emails in place of legacy SMTP settings (default: `false`)
+
+`NXF_ENABLE_FS_SYNC`
+: :::{versionadded} 23.10.0
+  :::
+: When enabled the job script will execute Linux `sync` command on job completion. This may be useful to synchronize the job state over shared file systems (default: `false`)
+
+`NXF_ENABLE_SECRETS`
+: :::{versionadded} 21.09.0-edge
+  :::
+: Enable Nextflow secrets features (default: `true`)
+
+`NXF_ENABLE_STRICT`
+: :::{versionadded} 22.05.0-edge
+  :::
+: Enable Nextflow *strict* execution mode (default: `false`)
+
+`NXF_ENABLE_VIRTUAL_THREADS`
+: :::{versionadded} 23.05.0-edge
+  :::
+: Enable the use of virtual threads in the Nextflow runtime (default: `false`)
+
+`NXF_EXECUTOR`
+: Defines the default process executor, e.g. `sge`
+
+`NXF_FILE_ROOT`
+: :::{versionadded} 23.05.0-edge
+  :::
+: The file storage path against which relative file paths are resolved.
+: For example, with `NXF_FILE_ROOT=/some/root/path`, the use of `file('foo')` will be resolved to the absolute path `/some/root/path/foo`. A remote root path can be specified using the usual protocol prefix, e.g. `NXF_FILE_ROOT=s3://my-bucket/data`. Files defined using an absolute path are not affected by this setting.
+
+`NXF_HOME`
+: Nextflow home directory (default: `$HOME/.nextflow`).
+
+`NXF_JAVA_HOME`
+: Defines the path location of the Java VM installation used to run Nextflow. This variable overrides the `JAVA_HOME` variable if defined.
+
+`NXF_JVM_ARGS`
+: :::{versionadded} 21.12.1-edge
+  :::
+: Allows the setting Java VM options. This is similar to `NXF_OPTS` however it's only applied the JVM running Nextflow and not to any java pre-launching commands.
+
+`NXF_LOG_FILE`
+: The filename of the Nextflow log (default: `.nextflow.log`)
+
+`NXF_OFFLINE`
+: When `true` prevents Nextflow from automatically downloading and updating remote project repositories (default: `false`).
+: :::{versionchanged} 23.09.0-edge
+  This option also disables the automatic version check (see `NXF_DISABLE_CHECK_LATEST`).
+  :::
+: :::{versionchanged} 23.11.0-edge
+  This option also prevents plugins from being downloaded. Plugin versions must be specified in offline mode, or else Nextflow will fail.
+  :::
+
+`NXF_OPTS`
+: Provides extra options for the Java and Nextflow runtime. It must be a blank separated list of `-Dkey[=value]` properties.
+
+`NXF_ORG`
+: Default `organization` prefix when looking for a hosted repository (default: `nextflow-io`).
+
+`NXF_PARAMS_FILE`
+: :::{versionadded} 20.10.0
+  :::
+: Defines the path location of the pipeline parameters file .
+
+`NXF_PID_FILE`
+: Name of the file where the process PID is saved when Nextflow is launched in background.
+
+`NXF_PLUGINS_DEFAULT`
+: Whether to use the default plugins when no plugins are specified in the Nextflow configuration (default: `true`).
+
+`NXF_PLUGINS_DIR`
+: The path where the plugin archives are loaded and stored (default: `$NXF_HOME/plugins`).
+
+`NXF_PLUGINS_TEST_REPOSITORY`
+: :::{versionadded} 23.04.0
+  :::
+: Defines a custom plugin registry or plugin release URL for testing plugins outside of the main registry. See {ref}`testing-plugins` for more information.
+
+`NXF_PUBLISH_FAIL_ON_ERROR`
+: :::{versionadded} 24.04.3
+  :::
+: Defines the default behavior of `publishDir.failOnError` setting. See {ref}`publishDir<process-publishdir>` directive for more information.
+
+`NXF_SCM_FILE`
+: :::{versionadded} 20.10.0
+  :::
+: Defines the path location of the SCM config file .
+
+`NXF_SINGULARITY_CACHEDIR`
+: Directory where remote Singularity images are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
+
+`NXF_SINGULARITY_LIBRARYDIR`
+: :::{versionadded} 21.09.0-edge
+  :::
+: Directory where remote Singularity images are retrieved. It should be a directory accessible to all compute nodes.
+
+`NXF_SPACK_CACHEDIR`
+: Directory where Spack environments are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
+
+`NXF_SPACK_ENABLED`
+: :::{versionadded} 23.02.0-edge
+  :::
+: Enable the use of Spack recipes defined by using the {ref}`process-spack` directive. (default: `false`).
+
+`NXF_TEMP`
+: Directory where temporary files are stored
+
+`NXF_TRACE`
+: Enable trace level logging for the specified packages. Equivalent to the `-trace` command-line option.
+
+`NXF_VER`
+: Defines which version of Nextflow to use.
+
+`NXF_WORK`
+: Directory where working files are stored (usually your *scratch* directory)
+
+`NXF_WRAPPER_STAGE_FILE_THRESHOLD`
+: :::{versionadded} 23.05.0-edge
+  :::
+: Defines the minimum size of the `.command.run` staging script for it to be written to a separate `.command.stage` file (default: `'1 MB'`).
+: This setting is useful for executors that impose a size limit on job scripts.
+
+## Proxy settings
+
+`FTP_PROXY`
+: :::{versionadded} 21.06.0-edge
+  :::
+: Defines the FTP proxy server. Proxy authentication is supported by providing the credentials in the proxy URL, e.g. `ftp://user:password@proxy-host.com:port`.
+
+`HTTP_PROXY`
+: Defines the HTTP proxy server.
+: :::{versionadded} 21.06.0-edge
+  Proxy authentication is supported by providing the credentials in the proxy URL, e.g. `http://user:password@proxy-host.com:port`.
+  :::
+
+`HTTPS_PROXY`
+: Defines the HTTPS proxy server.
+: :::{versionadded} 21.06.0-edge
+  Proxy authentication is supported by providing the credentials in the proxy URL, e.g. `https://user:password@proxy-host.com:port`.
+  :::
+
+`NO_PROXY`
+: Defines one or more host names that should not use the proxy server. Separate multiple names using a comma character.
diff --git a/docs/reference/feature-flags.md b/docs/reference/feature-flags.md
new file mode 100644
index 0000000000..616f1adfef
--- /dev/null
+++ b/docs/reference/feature-flags.md
@@ -0,0 +1,65 @@
+(config-feature-flags)=
+
+# Feature flags
+
+Feature flags are used to introduce experimental or other opt-in features. They can be specified in the pipeline script or the configuration file.
+
+`nextflow.enable.configProcessNamesValidation`
+: When `true`, prints a warning for every `withName:` process selector that doesn't match a process in the pipeline (default: `true`).
+
+`nextflow.enable.dsl`
+: Defines the DSL version to use (`1` or `2`).
+: :::{versionchanged} 22.03.0-edge
+  DSL2 was made the default DSL version.
+  :::
+: :::{versionchanged} 22.12.0-edge
+  DSL1 was removed.
+  :::
+
+`nextflow.enable.moduleBinaries`
+: When `true`, enables the use of modules with binary scripts. See {ref}`module-binaries` for more information.
+
+`nextflow.enable.strict`
+: :::{versionadded} 22.05.0-edge
+  :::
+: When `true`, the pipeline is executed in "strict" mode, which introduces the following rules:
+
+  - When reading a params file, Nextflow will fail if a dynamic param value references an undefined variable
+
+  - When merging params from a config file with params from the command line, Nextflow will fail if a param is specified from both sources but with different types
+
+  - When using the `join` operator, the `failOnDuplicate` option is `true` regardless of any user setting
+
+  - When using the `join` operator, the `failOnMismatch` option is `true` (unless `remainder` is also `true`) regardless of any user setting
+
+  - When using the `publishDir` process directive, the `failOnError` option is `true` regardless of any user setting
+
+  - In a process definition, Nextflow will fail if an input or output tuple has only one element
+
+  - In a process definition, Nextflow will fail if an output emit name is not a valid identifier (i.e. it should match the pattern `/[A-Za-z_][A-Za-z0-9_]*/`)
+
+  - During a process execution, Nextflow will fail if a received input tuple does not have the same number of elements as was declared
+
+  - During a process execution, Nextflow will fail if the `storeDir` directive is used with non-file outputs
+
+  - Nextflow will fail if a pipeline param is referenced before it is defined
+
+  - Nextflow will fail if multiple functions and/or processes with the same name are defined in a module script
+
+`nextflow.preview.output`
+: :::{versionadded} 24.04.0
+  :::
+: *Experimental: may change in a future release.*
+: When `true`, enables the use of the {ref}`workflow output definition <workflow-output-def>`.
+
+`nextflow.preview.recursion`
+: :::{versionadded} 21.11.0-edge
+  :::
+: *Experimental: may change in a future release.*
+: When `true`, enables process and workflow recursion. See [this GitHub discussion](https://github.com/nextflow-io/nextflow/discussions/2521) for more information.
+
+`nextflow.preview.topic`
+: :::{versionadded} 23.11.0-edge
+  :::
+: *Experimental: may change in a future release.*
+: When `true`, enables {ref}`topic channels <channel-topic>` feature.
diff --git a/docs/operator.md b/docs/reference/operator.md
similarity index 79%
rename from docs/operator.md
rename to docs/reference/operator.md
index 5a1aebf61b..3426e925c2 100644
--- a/docs/operator.md
+++ b/docs/reference/operator.md
@@ -2,18 +2,6 @@
 
 # Operators
 
-Nextflow **operators** are methods that allow you to manipulate channels. Every operator, with the exception of [set](#set) and [subscribe](#subscribe), produces one or more new channels, allowing you to chain operators to fit your needs.
-
-This page is a comprehensive reference for all Nextflow operators. However, if you are new to Nextflow, here are some suggested operators to learn for common use cases:
-
-- Filtering: [filter](#filter), [randomSample](#randomsample), [take](#take), [unique](#unique)
-- Reduction: [collect](#collect), [groupTuple](#grouptuple), [reduce](#reduce)
-- Text processing: [splitCsv](#splitcsv), [splitJson](#splitjson), [splitText](#splittext)
-- Combining channels: [combine](#combine), [concat](#concat), [join](#join), [mix](#mix)
-- Forking channels: [branch](#branch), [multiMap](#multimap)
-- Maths: [count](#count), [max](#max), [min](#min), [sum](#sum)
-- Other: [ifEmpty](#ifempty), [map](#map), [set](#set), [view](#view)
-
 (operator-branch)=
 
 ## branch
@@ -27,11 +15,11 @@ The `branch` operator forwards each item from a source channel to one of multipl
 
 The selection criteria is a {ref}`closure <script-closure>` that defines, for each output channel, a unique label followed by a boolean expression. When an item is received, it is routed to the first output channel whose expression evaluates to `true`. For example:
 
-```{literalinclude} snippets/branch.nf
-:language: groovy
+```{literalinclude} ../snippets/branch.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/branch.out
+```{literalinclude} ../snippets/branch.out
 :language: console
 ```
 
@@ -41,21 +29,21 @@ The above output may be printed in any order since the two `view` operations are
 
 A fallback condition can be specified using `true` as the last branch condition:
 
-```{literalinclude} snippets/branch-with-fallback.nf
-:language: groovy
+```{literalinclude} ../snippets/branch-with-fallback.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/branch-with-fallback.out
+```{literalinclude} ../snippets/branch-with-fallback.out
 :language: console
 ```
 
 The value emitted to each branch can be customized with an expression statement (or statements) after the branch condition:
 
-```{literalinclude} snippets/branch-with-mapper.nf
-:language: groovy
+```{literalinclude} ../snippets/branch-with-mapper.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/branch-with-mapper.out
+```{literalinclude} ../snippets/branch-with-mapper.out
 :language: console
 ```
 
@@ -65,11 +53,11 @@ When the `return` keyword is omitted, the value of the last expression statement
 
 The `branchCriteria()` method can be used to create a branch criteria as a variable that can be passed as an argument to any number of `branch` operations, as shown below:
 
-```{literalinclude} snippets/branch-criteria.nf
-:language: groovy
+```{literalinclude} ../snippets/branch-criteria.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/branch-criteria.out
+```{literalinclude} ../snippets/branch-criteria.out
 :language: console
 ```
 
@@ -85,11 +73,11 @@ This operator has multiple variants:
 
 : Emits each subset when `closingCondition` is satisfied. The closing condition can be a literal value, a {ref}`regular expression <script-regexp>`, a type qualifier (i.e. Java class), or a boolean predicate. For example:
 
-  ```{literalinclude} snippets/buffer-with-closing.nf
-  :language: groovy
+  ```{literalinclude} ../snippets/buffer-with-closing.nf
+  :language: nextflow
   ```
 
-  ```{literalinclude} snippets/buffer-with-closing.out
+  ```{literalinclude} ../snippets/buffer-with-closing.out
   :language: console
   ```
 
@@ -97,11 +85,11 @@ This operator has multiple variants:
 
 : Creates a new subset when `openingCondition` is satisfied and emits the subset when is `closingCondition` is satisfied. The opening and closing conditions can each be a literal value, a {ref}`regular expression <script-regexp>`, a type qualifier (i.e. Java class), or a boolean predicate. For example:
 
-  ```{literalinclude} snippets/buffer-with-opening-closing.nf
-  :language: groovy
+  ```{literalinclude} ../snippets/buffer-with-opening-closing.nf
+  :language: nextflow
   ```
 
-  ```{literalinclude} snippets/buffer-with-opening-closing.out
+  ```{literalinclude} ../snippets/buffer-with-opening-closing.out
   :language: console
   ```
 
@@ -109,21 +97,21 @@ This operator has multiple variants:
 
 : Emits a new subset for every `n` items. Remaining items are discarded. For example:
 
-  ```{literalinclude} snippets/buffer-with-size.nf
-  :language: groovy
+  ```{literalinclude} ../snippets/buffer-with-size.nf
+  :language: nextflow
   ```
 
-  ```{literalinclude} snippets/buffer-with-size.out
+  ```{literalinclude} ../snippets/buffer-with-size.out
   :language: console
   ```
 
   The `remainder` option can be used to emit any remaining items as a partial subset:
 
-  ```{literalinclude} snippets/buffer-with-size-remainder.nf
-  :language: groovy
+  ```{literalinclude} ../snippets/buffer-with-size-remainder.nf
+  :language: nextflow
   ```
 
-  ```{literalinclude} snippets/buffer-with-size-remainder.out
+  ```{literalinclude} ../snippets/buffer-with-size-remainder.out
   :language: console
   ```
 
@@ -131,11 +119,11 @@ This operator has multiple variants:
 
 : Emits a new subset for every `n` items, skipping `m` items before collecting each subset. For example:
 
-  ```{literalinclude} snippets/buffer-with-size-skip.nf
-  :language: groovy
+  ```{literalinclude} ../snippets/buffer-with-size-skip.nf
+  :language: nextflow
   ```
 
-  ```{literalinclude} snippets/buffer-with-size-skip.out
+  ```{literalinclude} ../snippets/buffer-with-size-skip.out
   :language: console
   ```
 
@@ -155,21 +143,21 @@ This operator has multiple variants:
 
 : Collects items into groups of `size` items:
 
-  ```{literalinclude} snippets/collate.nf
-  :language: groovy
+  ```{literalinclude} ../snippets/collate.nf
+  :language: nextflow
   ```
 
-  ```{literalinclude} snippets/collate.out
+  ```{literalinclude} ../snippets/collate.out
   :language: console
   ```
 
   By default, any remaining items are emitted as a partial group. You can specify `false` as the second parameter to discard them instead:
 
-  ```{literalinclude} snippets/collate-with-no-remainder.nf
-  :language: groovy
+  ```{literalinclude} ../snippets/collate-with-no-remainder.nf
+  :language: nextflow
   ```
 
-  ```{literalinclude} snippets/collate-with-no-remainder.out
+  ```{literalinclude} ../snippets/collate-with-no-remainder.out
   :language: console
   ```
 
@@ -181,11 +169,11 @@ This operator has multiple variants:
 
 : Collects items into groups of `size` items using a *sliding window* that moves by `step` items at a time:
 
-  ```{literalinclude} snippets/collate-with-step.nf
-  :language: groovy
+  ```{literalinclude} ../snippets/collate-with-step.nf
+  :language: nextflow
   ```
 
-  ```{literalinclude} snippets/collate-with-step.out
+  ```{literalinclude} ../snippets/collate-with-step.out
   :language: console
   ```
 
@@ -201,21 +189,21 @@ See also: [buffer](#buffer)
 
 The `collect` operator collects all items from a source channel into a list and emits it as a single item:
 
-```{literalinclude} snippets/collect.nf
-:language: groovy
+```{literalinclude} ../snippets/collect.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/collect.out
+```{literalinclude} ../snippets/collect.out
 :language: console
 ```
 
 An optional {ref}`closure <script-closure>` can be used to transform each item before it is collected:
 
-```{literalinclude} snippets/collect-with-mapper.nf
-:language: groovy
+```{literalinclude} ../snippets/collect-with-mapper.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/collect-with-mapper.out
+```{literalinclude} ../snippets/collect-with-mapper.out
 :language: console
 ```
 
@@ -237,23 +225,23 @@ The `collectFile` operator collects the items from a source channel and saves th
 
 This operator has multiple variants:
 
-`collectFile( name: '...', options = [:] )`
+`collectFile( name: '...', [options] )`
 
 : Collects the items and saves them to a single file specified by the `name` option:
 
-  ```{literalinclude} snippets/collectfile.nf
-  :language: groovy
+  ```{literalinclude} ../snippets/collectfile.nf
+  :language: nextflow
   ```
 
-`collectFile( closure, options = [:] )`
+`collectFile( closure, [options] )`
 
 : Collects the items into groups and saves each group to a file, using a grouping criteria. The grouping criteria is a {ref}`closure <script-closure>` that maps each item to a pair, where the first element is the file name for the group and the second element is the content to be appended to that file. For example:
 
-  ```{literalinclude} snippets/collectfile-closure.nf
-  :language: groovy
+  ```{literalinclude} ../snippets/collectfile-closure.nf
+  :language: nextflow
   ```
 
-  ```{literalinclude} snippets/collectfile-closure.out
+  ```{literalinclude} ../snippets/collectfile-closure.out
   :language: console
   ```
 
@@ -261,14 +249,14 @@ This operator has multiple variants:
 
 The following example shows how to use a closure to collect and sort all sequences in a FASTA file from shortest to longest:
 
-```groovy
+```nextflow
 Channel
     .fromPath('/data/sequences.fa')
     .splitFasta( record: [id: true, sequence: true] )
-    .collectFile( name: 'result.fa', sort: { it.size() } ) {
-        it.sequence
+    .collectFile( name: 'result.fa', sort: { v -> v.size() } ) {
+        v -> v.sequence
     }
-    .view { it.text }
+    .view { fa -> fa.text }
 ```
 
 :::{warning}
@@ -323,21 +311,21 @@ The `combine` operator produces the combinations (i.e. cross product, "Cartesian
 
 For example:
 
-```{literalinclude} snippets/combine.nf
-:language: groovy
+```{literalinclude} ../snippets/combine.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/combine.out
+```{literalinclude} ../snippets/combine.out
 :language: console
 ```
 
 The `by` option can be used to combine items that share a matching key. The value should be the zero-based index of the tuple, or a list of indices. For example:
 
-```{literalinclude} snippets/combine-by.nf
-:language: groovy
+```{literalinclude} ../snippets/combine-by.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/combine-by.out
+```{literalinclude} ../snippets/combine-by.out
 :language: console
 ```
 
@@ -365,11 +353,11 @@ In other words, given *N* channels, the items from the *i+1*-th channel are emit
 
 For example:
 
-```{literalinclude} snippets/concat.nf
-:language: groovy
+```{literalinclude} ../snippets/concat.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/concat.out
+```{literalinclude} ../snippets/concat.out
 :language: console
 ```
 
@@ -383,37 +371,37 @@ See also: [mix](#mix)
 
 The `count` operator computes the total number of items in a source channel and emits it:
 
-```{literalinclude} snippets/count.nf
-:language: groovy
+```{literalinclude} ../snippets/count.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/count.out
+```{literalinclude} ../snippets/count.out
 :language: console
 ```
 
 An optional filter can be provided to select which items to count. The selection criteria can be a literal value, a {ref}`regular expression <script-regexp>`, a type qualifier (i.e. Java class), or a boolean predicate. For example:
 
-```{literalinclude} snippets/count-with-filter-number.nf
-:language: groovy
+```{literalinclude} ../snippets/count-with-filter-number.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/count-with-filter-number.out
+```{literalinclude} ../snippets/count-with-filter-number.out
 :language: console
 ```
 
-```{literalinclude} snippets/count-with-filter-regex.nf
-:language: groovy
+```{literalinclude} ../snippets/count-with-filter-regex.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/count-with-filter-regex.out
+```{literalinclude} ../snippets/count-with-filter-regex.out
 :language: console
 ```
 
-```{literalinclude} snippets/count-with-filter-closure.nf
-:language: groovy
+```{literalinclude} ../snippets/count-with-filter-closure.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/count-with-filter-closure.out
+```{literalinclude} ../snippets/count-with-filter-closure.out
 :language: console
 ```
 
@@ -459,21 +447,21 @@ The `cross` operator emits every pairwise combination of two channels for which
 
 By default, the key is defined as the first entry in a list or map, or the value itself for any other data type. For example:
 
-```{literalinclude} snippets/cross.nf
-:language: groovy
+```{literalinclude} ../snippets/cross.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/cross.out
+```{literalinclude} ../snippets/cross.out
 :language: console
 ```
 
 An optional closure can be used to define the matching key for each item:
 
-```{literalinclude} snippets/cross-with-mapper.nf
-:language: groovy
+```{literalinclude} ../snippets/cross-with-mapper.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/cross-with-mapper.out
+```{literalinclude} ../snippets/cross-with-mapper.out
 :language: console
 ```
 
@@ -490,21 +478,21 @@ See also: [combine](#combine)
 
 The `distinct` operator forwards a source channel with *consecutively* repeated items removed, such that each emitted item is different from the preceding one:
 
-```{literalinclude} snippets/distinct.nf
-:language: groovy
+```{literalinclude} ../snippets/distinct.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/distinct.out
+```{literalinclude} ../snippets/distinct.out
 :language: console
 ```
 
 An optional {ref}`closure <script-closure>` can be used to transform each value before it is evaluated for distinct-ness:
 
-```{literalinclude} snippets/distinct-with-mapper.nf
-:language: groovy
+```{literalinclude} ../snippets/distinct-with-mapper.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/distinct-with-mapper.out
+```{literalinclude} ../snippets/distinct-with-mapper.out
 :language: console
 ```
 
@@ -520,8 +508,8 @@ The `dump` operator prints each item in a source channel when the pipeline is ex
 
 The `tag` option can be used to select which channels to dump:
 
-```{literalinclude} snippets/dump.nf
-:language: groovy
+```{literalinclude} ../snippets/dump.nf
+:language: nextflow
 ```
 
 Then, you can run your pipeline with `-dump-channels foo` or `-dump-channels bar` to dump the content of either channel. Multiple tag names can be specified as a comma-separated list.
@@ -536,6 +524,8 @@ Available options:
 `tag`
 : Associate the channel with a tag that can be specified with the `-dump-channels` option to select which channels to dump.
 
+(operator-filter)=
+
 ## filter
 
 *Returns: queue channel or value channel, matching the source type*
@@ -544,31 +534,31 @@ The `filter` operator emits the items from a source channel that satisfy a condi
 
 The following example filters a channel with a regular expression that only matches strings beginning with `a`:
 
-```{literalinclude} snippets/filter-regex.nf
-:language: groovy
+```{literalinclude} ../snippets/filter-regex.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/filter-regex.out
+```{literalinclude} ../snippets/filter-regex.out
 :language: console
 ```
 
 The following example filters a channel with the `Number` type qualifier so that only numbers are emitted:
 
-```{literalinclude} snippets/filter-type.nf
-:language: groovy
+```{literalinclude} ../snippets/filter-type.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/filter-type.out
+```{literalinclude} ../snippets/filter-type.out
 :language: console
 ```
 
 The following example filters a channel using a boolean predicate, which is a {ref}`closure <script-closure>` that returns a boolean value. In this case, the predicate is used to select only odd numbers:
 
-```{literalinclude} snippets/filter-closure.nf
-:language: groovy
+```{literalinclude} ../snippets/filter-closure.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/filter-closure.out
+```{literalinclude} ../snippets/filter-closure.out
 :language: console
 ```
 
@@ -580,8 +570,8 @@ The following example filters a channel using a boolean predicate, which is a {r
 
 The `first` operator emits the first item in a source channel, or the first item that matches a condition. The condition can be a {ref}`regular expression<script-regexp>`, a type qualifier (i.e. Java class), or a boolean predicate. For example:
 
-```{literalinclude} snippets/first.nf
-:language: groovy
+```{literalinclude} ../snippets/first.nf
+:language: nextflow
 ```
 
 (operator-flatmap)=
@@ -594,21 +584,21 @@ The `flatMap` operator applies a *mapping function* to each item from a source c
 
 When the mapping function returns a list, each element in the list is emitted separately:
 
-```{literalinclude} snippets/flatmap-list.nf
-:language: groovy
+```{literalinclude} ../snippets/flatmap-list.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/flatmap-list.out
+```{literalinclude} ../snippets/flatmap-list.out
 :language: console
 ```
 
 When the mapping function returns a map, each key-value pair in the map is emitted separately:
 
-```{literalinclude} snippets/flatmap-map.nf
-:language: groovy
+```{literalinclude} ../snippets/flatmap-map.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/flatmap-map.out
+```{literalinclude} ../snippets/flatmap-map.out
 :language: console
 ```
 
@@ -620,11 +610,11 @@ When the mapping function returns a map, each key-value pair in the map is emitt
 
 The `flatten` operator flattens each item from a source channel that is a list or other collection, such that each element in each collection is emitted separately:
 
-```{literalinclude} snippets/flatten.nf
-:language: groovy
+```{literalinclude} ../snippets/flatten.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/flatten.out
+```{literalinclude} ../snippets/flatten.out
 :language: console
 ```
 
@@ -644,31 +634,31 @@ To be more precise, the operator transforms a sequence of tuples like *(K, V, W,
 
 For example:
 
-```{literalinclude} snippets/grouptuple.nf
-:language: groovy
+```{literalinclude} ../snippets/grouptuple.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/grouptuple.out
+```{literalinclude} ../snippets/grouptuple.out
 :language: console
 ```
 
 By default, the first element of each tuple is used as the grouping key. The `by` option can be used to specify a different index, or list of indices. For example, to group by the second element of each tuple:
 
-```{literalinclude} snippets/grouptuple-by.nf
-:language: groovy
+```{literalinclude} ../snippets/grouptuple-by.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/grouptuple-by.out
+```{literalinclude} ../snippets/grouptuple-by.out
 :language: console
 ```
 
 By default, if you don't specify a size, the `groupTuple` operator will not emit any groups until *all* inputs have been received. If possible, you should always try to specify the number of expected elements in each group using the `size` option, so that each group can be emitted as soon as it's ready. In cases where the size of each group varies based on the grouping key, you can use the built-in `groupKey()` function, which allows you to define a different expected size for each group:
 
-```{literalinclude} snippets/grouptuple-groupkey.nf
-:language: groovy
+```{literalinclude} ../snippets/grouptuple-groupkey.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/grouptuple-groupkey.out
+```{literalinclude} ../snippets/grouptuple-groupkey.out
 :language: console
 ```
 
@@ -700,19 +690,19 @@ Available options:
 
 The `ifEmpty` operator emits a source channel, or a default value if the source channel is *empty* (doesn't emit any value):
 
-```{literalinclude} snippets/ifempty-1.nf
-:language: groovy
+```{literalinclude} ../snippets/ifempty-1.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/ifempty-1.out
+```{literalinclude} ../snippets/ifempty-1.out
 :language: console
 ```
 
-```{literalinclude} snippets/ifempty-2.nf
-:language: groovy
+```{literalinclude} ../snippets/ifempty-2.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/ifempty-2.out
+```{literalinclude} ../snippets/ifempty-2.out
 :language: console
 ```
 
@@ -732,11 +722,11 @@ To be more precise, the operator transforms a sequence of tuples like *(K, V1, V
 
 For example:
 
-```{literalinclude} snippets/join.nf
-:language: groovy
+```{literalinclude} ../snippets/join.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/join.out
+```{literalinclude} ../snippets/join.out
 :language: console
 ```
 
@@ -744,11 +734,11 @@ By default, the first element of each item is used as the key. The `by` option c
 
 By default, unmatched items are discarded. The `remainder` option can be used to emit them at the end:
 
-```{literalinclude} snippets/join-with-remainder.nf
-:language: groovy
+```{literalinclude} ../snippets/join-with-remainder.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/join-with-remainder.out
+```{literalinclude} ../snippets/join-with-remainder.out
 :language: console
 ```
 
@@ -776,11 +766,11 @@ See also: [combine](#combine), [cross](#cross)
 
 The `last` operator emits the last item from a source channel:
 
-```{literalinclude} snippets/last.nf
-:language: groovy
+```{literalinclude} ../snippets/last.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/last.out
+```{literalinclude} ../snippets/last.out
 :language: console
 ```
 
@@ -792,11 +782,11 @@ The `last` operator emits the last item from a source channel:
 
 The `map` operator applies a *mapping function* to each item from a source channel:
 
-```{literalinclude} snippets/map.nf
-:language: groovy
+```{literalinclude} ../snippets/map.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/map.out
+```{literalinclude} ../snippets/map.out
 :language: console
 ```
 
@@ -808,11 +798,11 @@ The `map` operator applies a *mapping function* to each item from a source chann
 
 The `max` operator emits the item with the greatest value from a source channel:
 
-```{literalinclude} snippets/max.nf
-:language: groovy
+```{literalinclude} ../snippets/max.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/max.out
+```{literalinclude} ../snippets/max.out
 :language: console
 ```
 
@@ -820,19 +810,19 @@ An optional {ref}`closure <script-closure>` can be used to control how the items
 
 The following examples show how to find the longest string in a channel:
 
-```{literalinclude} snippets/max-with-mapper.nf
-:language: groovy
+```{literalinclude} ../snippets/max-with-mapper.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/max-with-mapper.out
+```{literalinclude} ../snippets/max-with-mapper.out
 :language: console
 ```
 
-```{literalinclude} snippets/max-with-comparator.nf
-:language: groovy
+```{literalinclude} ../snippets/max-with-comparator.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/max-with-comparator.out
+```{literalinclude} ../snippets/max-with-comparator.out
 :language: console
 ```
 
@@ -844,21 +834,21 @@ The following examples show how to find the longest string in a channel:
 
 The `merge` operator joins the items from two or more channels into a new channel:
 
-```{literalinclude} snippets/merge.nf
-:language: groovy
+```{literalinclude} ../snippets/merge.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/merge.out
+```{literalinclude} ../snippets/merge.out
 :language: console
 ```
 
 An optional closure can be used to control how two items are merged:
 
-```{literalinclude} snippets/merge-with-mapper.nf
-:language: groovy
+```{literalinclude} ../snippets/merge-with-mapper.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/merge-with-mapper.out
+```{literalinclude} ../snippets/merge-with-mapper.out
 :language: console
 ```
 
@@ -882,11 +872,11 @@ You should always use a matching key (e.g. sample ID) to merge multiple channels
 
 The `min` operator emits the item with the lowest value from a source channel:
 
-```{literalinclude} snippets/min.nf
-:language: groovy
+```{literalinclude} ../snippets/min.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/min.out
+```{literalinclude} ../snippets/min.out
 :language: console
 ```
 
@@ -894,19 +884,19 @@ An optional {ref}`closure <script-closure>` can be used to control how the items
 
 The following examples show how to find the shortest string in a channel:
 
-```{literalinclude} snippets/min-with-mapper.nf
-:language: groovy
+```{literalinclude} ../snippets/min-with-mapper.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/min-with-mapper.out
+```{literalinclude} ../snippets/min-with-mapper.out
 :language: console
 ```
 
-```{literalinclude} snippets/min-with-comparator.nf
-:language: groovy
+```{literalinclude} ../snippets/min-with-comparator.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/min-with-comparator.out
+```{literalinclude} ../snippets/min-with-comparator.out
 :language: console
 ```
 
@@ -918,11 +908,11 @@ The following examples show how to find the shortest string in a channel:
 
 The `mix` operator emits the items from two or more source channels into a single output channel:
 
-```{literalinclude} snippets/mix.nf
-:language: groovy
+```{literalinclude} ../snippets/mix.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/mix.out
+```{literalinclude} ../snippets/mix.out
 :language: console
 ```
 
@@ -954,21 +944,21 @@ The multi-map criteria is a {ref}`closure <script-closure>` that defines, for ea
 
 For example:
 
-```{literalinclude} snippets/multimap.nf
-:language: groovy
+```{literalinclude} ../snippets/multimap.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/multimap.out
+```{literalinclude} ../snippets/multimap.out
 :language: console
 ```
 
 Multiple labels can share the same mapping expression using the following shorthand:
 
-```{literalinclude} snippets/multimap-shared.nf
-:language: groovy
+```{literalinclude} ../snippets/multimap-shared.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/multimap-shared.out
+```{literalinclude} ../snippets/multimap-shared.out
 :language: console
 ```
 
@@ -976,8 +966,8 @@ The above example creates two channels as before, but now they both receive the
 
 You can use the `multiMapCriteria()` method to create a multi-map criteria as a variable that can be passed as an argument to any number of `multiMap` operations, as shown below:
 
-```{literalinclude} snippets/multimap-criteria.nf
-:language: groovy
+```{literalinclude} ../snippets/multimap-criteria.nf
+:language: nextflow
 ```
 
 :::{note}
@@ -992,16 +982,16 @@ If you use `multiMap` to split a tuple or map into multiple channels, it is reco
 
 The `randomSample` operator emits a randomly-selected subset of items from a source channel:
 
-```{literalinclude} snippets/random-sample.nf
-:language: groovy
+```{literalinclude} ../snippets/random-sample.nf
+:language: nextflow
 ```
 
 The above snippet will print 10 randomly-selected numbers between 1 and 100 (without replacement).
 
 An optional second parameter can be used to set the initial *seed* for the random number generator, which ensures that the `randomSample` operator produces the same pseudo-random sequence across runs:
 
-```{literalinclude} snippets/random-sample-with-seed.nf
-:language: groovy
+```{literalinclude} ../snippets/random-sample-with-seed.nf
+:language: nextflow
 ```
 
 The above example will print 10 randomly-selected numbers between 1 and 100 (without replacement). Each subsequent script execution will produce the same sequence.
@@ -1016,21 +1006,21 @@ The `reduce` operator applies an *accumulator function* sequentially to each ite
 
 For example:
 
-```{literalinclude} snippets/reduce.nf
-:language: groovy
+```{literalinclude} ../snippets/reduce.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/reduce.out
+```{literalinclude} ../snippets/reduce.out
 :language: console
 ```
 
 By default, the first item is used as the initial accumulated value. You can optionally specify a different initial value as shown below:
 
-```{literalinclude} snippets/reduce-with-initial-value.nf
-:language: groovy
+```{literalinclude} ../snippets/reduce-with-initial-value.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/reduce-with-initial-value.out
+```{literalinclude} ../snippets/reduce-with-initial-value.out
 :language: console
 ```
 
@@ -1042,13 +1032,13 @@ By default, the first item is used as the initial accumulated value. You can opt
 
 The `set` operator assigns a source channel to a variable, whose name is specified as a closure parameter:
 
-```groovy
+```nextflow
 Channel.of(10, 20, 30).set { my_channel }
 ```
 
 Using `set` is semantically equivalent to assigning a variable:
 
-```groovy
+```nextflow
 my_channel = Channel.of(10, 20, 30)
 ```
 
@@ -1064,11 +1054,11 @@ The `splitCsv` operator parses and splits [CSV-formatted](http://en.wikipedia.or
 
 For example:
 
-```{literalinclude} snippets/splitcsv.nf
-:language: groovy
+```{literalinclude} ../snippets/splitcsv.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/splitcsv.out
+```{literalinclude} ../snippets/splitcsv.out
 :language: console
 ```
 
@@ -1076,21 +1066,21 @@ The above example shows hows CSV text is parsed and split into individual rows,
 
 When the CSV begins with a header line defining the column names, and the `header` option is `true`, each row is returned as a map instead:
 
-```{literalinclude} snippets/splitcsv-with-header.nf
-:language: groovy
+```{literalinclude} ../snippets/splitcsv-with-header.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/splitcsv-with-header.out
+```{literalinclude} ../snippets/splitcsv-with-header.out
 :language: console
 ```
 
 The `header` option can also just be a list of columns:
 
-```{literalinclude} snippets/splitcsv-with-columns.nf
-:language: groovy
+```{literalinclude} ../snippets/splitcsv-with-columns.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/splitcsv-with-columns.out
+```{literalinclude} ../snippets/splitcsv-with-columns.out
 :language: console
 ```
 
@@ -1136,7 +1126,7 @@ The `splitFasta` operator splits [FASTA-formatted](http://en.wikipedia.org/wiki/
 
 The `by` option can be used to group sequences into chunks of a given size. The following example shows how to read a FASTA file and split it into chunks of 10 sequences each:
 
-```groovy
+```nextflow
 Channel
      .fromPath('misc/sample.fa')
      .splitFasta( by: 10 )
@@ -1149,7 +1139,7 @@ Chunks are stored in memory by default. When splitting large files, specify `fil
 
 The `record` option can be used to split FASTA content into *records* instead of text chunks. Each record is a map that allows you to access the FASTA sequence data with ease. For example:
 
-```groovy
+```nextflow
 Channel
      .fromPath('misc/sample.fa')
      .splitFasta( record: [id: true, seqString: true] )
@@ -1208,7 +1198,7 @@ The `splitFasta` operator splits [FASTQ formatted](http://en.wikipedia.org/wiki/
 
 The `by` option can be used to group sequences into chunks of a given size. The following example shows how to read a FASTQ file and split it into chunks of 10 sequences each:
 
-```groovy
+```nextflow
 Channel
     .fromPath('misc/sample.fastq')
     .splitFastq( by: 10 )
@@ -1221,7 +1211,7 @@ Chunks are stored in memory by default. When splitting large files, specify `fil
 
 The `record` option can be used to split FASTQ content into *records* instead of text chunks. Each record is a map that allows you to access the FASTQ sequence data with ease. For example:
 
-```groovy
+```nextflow
 Channel
     .fromPath('misc/sample.fastq')
     .splitFastq( record: true )
@@ -1230,7 +1220,7 @@ Channel
 
 The `pe` option can be used to split paired-end FASTQ files. The source channel must emit tuples containing the file pairs. For example:
 
-```groovy
+```nextflow
 Channel
     .fromFilePairs('/my/data/SRR*_{1,2}.fastq', flat: true)
     .splitFastq(by: 100_000, pe: true, file: true)
@@ -1291,31 +1281,31 @@ The `splitJson` operator splits [JSON formatted](https://en.wikipedia.org/wiki/J
 
 If the source item is a JSON array, each element of the array will be emitted:
 
-```{literalinclude} snippets/splitjson-array.nf
-:language: groovy
+```{literalinclude} ../snippets/splitjson-array.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/splitjson-array.out
+```{literalinclude} ../snippets/splitjson-array.out
 :language: console
 ```
 
 If the source item is a JSON object, each key-value pair will be emitted as a map with the properties `key`  and `value`:
 
-```{literalinclude} snippets/splitjson-object.nf
-:language: groovy
+```{literalinclude} ../snippets/splitjson-object.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/splitjson-object.out
+```{literalinclude} ../snippets/splitjson-object.out
 :language: console
 ```
 
 The `path` option can be used to query a section of the JSON document to parse and split:
 
-```{literalinclude} snippets/splitjson-with-path.nf
-:language: groovy
+```{literalinclude} ../snippets/splitjson-with-path.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/splitjson-with-path.out
+```{literalinclude} ../snippets/splitjson-with-path.out
 :language: console
 ```
 
@@ -1337,7 +1327,7 @@ See also: [countJson](#countjson)
 
 The `splitText` operator splits multi-line text content from a source channel into chunks of *N* lines:
 
-```groovy
+```nextflow
 Channel
     .fromPath('/some/path/*.txt')
     .splitText()
@@ -1348,22 +1338,22 @@ The above example loads a collection of text files, splits the content of each f
 
 The `by` option can be used to emit chunks of *N* lines:
 
-```groovy
+```nextflow
 Channel
     .fromPath('/some/path/*.txt')
     .splitText( by: 10 )
-    .subscribe {
-        print it;
+    .subscribe { chunk ->
+        print chunk
         print "--- end of the chunk ---\n"
     }
 ```
 
 An optional {ref}`closure <script-closure>` can be used to transform each text chunk produced by the operator. The following example shows how to split text files into chunks of 10 lines and transform them to uppercase letters:
 
-```groovy
+```nextflow
 Channel
     .fromPath('/some/path/*.txt')
-    .splitText( by: 10 ) { it.toUpperCase() }
+    .splitText( by: 10 ) { v -> v.toUpperCase() }
     .view()
 ```
 
@@ -1403,38 +1393,32 @@ See also: [countLines](#countlines)
 
 ## subscribe
 
-*Returns: the source channel*
+*Returns: nothing*
 
 The `subscribe` operator invokes a custom function for each item from a source channel:
 
-```{literalinclude} snippets/subscribe.nf
-:language: groovy
+```{literalinclude} ../snippets/subscribe.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/subscribe.out
-:language: console
-```
-
-The closure parameter can be defined explicitly if needed, using a name other than `it` and, optionally, the expected type:
-
-```{literalinclude} snippets/subscribe-with-param.nf
-:language: groovy
-```
-
-```{literalinclude} snippets/subscribe-with-param.out
+```{literalinclude} ../snippets/subscribe.out
 :language: console
 ```
 
 The `subscribe` operator supports multiple types of event handlers:
 
-```{literalinclude} snippets/subscribe-with-on-complete.nf
-:language: groovy
+```{literalinclude} ../snippets/subscribe-with-on-complete.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/subscribe-with-on-complete.out
+```{literalinclude} ../snippets/subscribe-with-on-complete.out
 :language: console
 ```
 
+:::{note}
+Unlike most operators, `subscribe` is a *terminal operator* and does not emit any values. It should only be used for *side effects*, such as printing to the console, writing to a file, or making HTTP requests.
+:::
+
 Available options:
 
 `onNext`
@@ -1454,21 +1438,21 @@ Available options:
 
 The `sum` operator emits the sum of all items in a source channel:
 
-```{literalinclude} snippets/sum.nf
-:language: groovy
+```{literalinclude} ../snippets/sum.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/sum.out
+```{literalinclude} ../snippets/sum.out
 :language: console
 ```
 
 An optional {ref}`closure <script-closure>` can be used to transform each item before it is added to the sum:
 
-```{literalinclude} snippets/sum-with-mapper.nf
-:language: groovy
+```{literalinclude} ../snippets/sum-with-mapper.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/sum-with-mapper.out
+```{literalinclude} ../snippets/sum-with-mapper.out
 :language: console
 ```
 
@@ -1480,11 +1464,11 @@ An optional {ref}`closure <script-closure>` can be used to transform each item b
 
 The `take` operator takes the first *N* items from a source channel:
 
-```{literalinclude} snippets/take.nf
-:language: groovy
+```{literalinclude} ../snippets/take.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/take.out
+```{literalinclude} ../snippets/take.out
 :language: console
 ```
 
@@ -1500,11 +1484,11 @@ See also: [until](#until)
 
 The `tap` operator assigns a source channel to a variable, and emits the source channel. It is a useful way to extract intermediate output channels from a chain of operators. For example:
 
-```{literalinclude} snippets/tap.nf
-:language: groovy
+```{literalinclude} ../snippets/tap.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/tap.out
+```{literalinclude} ../snippets/tap.out
 :language: console
 ```
 
@@ -1516,19 +1500,19 @@ See also: [set](#set)
 
 The `toInteger` operator converts string values from a source channel to integer values:
 
-```{literalinclude} snippets/tointeger.nf
-:language: groovy
+```{literalinclude} ../snippets/tointeger.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/tointeger.out
+```{literalinclude} ../snippets/tointeger.out
 :language: console
 ```
 
 :::{note}
 `toInteger` is equivalent to:
 
-```groovy
-map { it -> it as Integer }
+```nextflow
+map { v -> v as Integer }
 ```
 :::
 
@@ -1542,11 +1526,11 @@ You can also use `toLong`, `toFloat`, and `toDouble` to convert to other numeric
 
 The `toList` operator collects all the items from a source channel into a list and emits the list as a single item:
 
-```{literalinclude} snippets/tolist.nf
-:language: groovy
+```{literalinclude} ../snippets/tolist.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/tolist.out
+```{literalinclude} ../snippets/tolist.out
 :language: console
 ```
 
@@ -1558,7 +1542,7 @@ There are two main differences between `toList` and `collect`:
 
 In other words, `toList` is equivalent to:
 
-```groovy
+```nextflow
 collect(flat: false).ifEmpty([])
 ```
 :::
@@ -1571,28 +1555,28 @@ See also: [collect](#collect)
 
 The `toSortedList` operator collects all the items from a source channel into a sorted list and emits the list as a single item:
 
-```{literalinclude} snippets/tosortedlist.nf
-:language: groovy
+```{literalinclude} ../snippets/tosortedlist.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/tosortedlist.out
+```{literalinclude} ../snippets/tosortedlist.out
 :language: console
 ```
 
 An optional closure can be used to control how items are compared when sorting. For example, to sort tuples by their second element in descending order:
 
-```{literalinclude} snippets/tosortedlist-with-comparator.nf
-:language: groovy
+```{literalinclude} ../snippets/tosortedlist-with-comparator.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/tosortedlist-with-comparator.out
+```{literalinclude} ../snippets/tosortedlist-with-comparator.out
 :language: console
 ```
 
 :::{note}
 `toSortedList` is equivalent to:
 
-```groovy
+```nextflow
 collect(flat: false, sort: true).ifEmpty([])
 ```
 :::
@@ -1609,31 +1593,31 @@ To be more precise, the operator transforms a sequence of tuples like *(K, list(
 
 For example:
 
-```{literalinclude} snippets/transpose-1.nf
-:language: groovy
+```{literalinclude} ../snippets/transpose-1.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/transpose-1.out
+```{literalinclude} ../snippets/transpose-1.out
 :language: console
 ```
 
 If each source item has more than two elements, these will be flattened by the first element in the item, and a new item will be emitted only when it is complete:
 
-```{literalinclude} snippets/transpose-2.nf
-:language: groovy
+```{literalinclude} ../snippets/transpose-2.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/transpose-2.out
+```{literalinclude} ../snippets/transpose-2.out
 :language: console
 ```
 
 The `remainder` option can be used to emit any incomplete items:
 
-```{literalinclude} snippets/transpose-2-with-remainder.nf
-:language: groovy
+```{literalinclude} ../snippets/transpose-2-with-remainder.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/transpose-2-with-remainder.out
+```{literalinclude} ../snippets/transpose-2-with-remainder.out
 :language: console
 ```
 
@@ -1647,27 +1631,29 @@ Available options:
 
 See also: [groupTuple](#grouptuple)
 
+(operator-unique)=
+
 ## unique
 
 *Returns: queue channel or value channel, matching the source type*
 
 The `unique` operator emits the unique items from a source channel:
 
-```{literalinclude} snippets/unique.nf
-:language: groovy
+```{literalinclude} ../snippets/unique.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/unique.out
+```{literalinclude} ../snippets/unique.out
 :language: console
 ```
 
 An optional {ref}`closure <script-closure>` can be used to transform each item before it is evaluated for uniqueness:
 
-```{literalinclude} snippets/unique-with-mapper.nf
-:language: groovy
+```{literalinclude} ../snippets/unique-with-mapper.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/unique-with-mapper.out
+```{literalinclude} ../snippets/unique-with-mapper.out
 :language: console
 ```
 
@@ -1685,11 +1671,11 @@ See also: [distinct](#distinct)
 
 The `until` operator emits each item from a source channel until a stopping condition is satisfied:
 
-```{literalinclude} snippets/until.nf
-:language: groovy
+```{literalinclude} ../snippets/until.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/until.out
+```{literalinclude} ../snippets/until.out
 :language: console
 ```
 
@@ -1703,21 +1689,21 @@ See also: [take](#take)
 
 The `view` operator prints each item from a source channel to standard output:
 
-```{literalinclude} snippets/view.nf
-:language: groovy
+```{literalinclude} ../snippets/view.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/view.out
+```{literalinclude} ../snippets/view.out
 :language: console
 ```
 
 An optional closure can be used to transform each item before it is printed:
 
-```{literalinclude} snippets/view-with-mapper.nf
-:language: groovy
+```{literalinclude} ../snippets/view-with-mapper.nf
+:language: nextflow
 ```
 
-```{literalinclude} snippets/view-with-mapper.out
+```{literalinclude} ../snippets/view-with-mapper.out
 :language: console
 ```
 
diff --git a/docs/reference/process.md b/docs/reference/process.md
new file mode 100644
index 0000000000..7383c8d5eb
--- /dev/null
+++ b/docs/reference/process.md
@@ -0,0 +1,1672 @@
+(process-reference)=
+
+# Process reference
+
+This page lists the task properties, input/output methods, and directives available in {ref}`process <process-page>` definitions.
+
+## Task properties
+
+The following task properties are defined in the process body:
+
+`task.attempt`
+: The current task attempt.
+
+`task.exitStatus`
+: The exit code of the task script. Only applicable for processes with a `script:` or `shell:` block.
+: Since the exit code is only available after the task has been executed, it can only be used by certain process directives such as [errorStrategy](#errorstrategy).
+
+`task.hash`
+: *Available only in `exec:` blocks*
+: The task unique hash ID.
+
+`task.id`
+: The pipeline-level task index. Corresponds to `task_id` in the {ref}`execution trace <trace-report>`.
+
+`task.index`
+: The process-level task index.
+
+`task.name`
+: *Available only in `exec:` blocks*
+: The current task name.
+
+`task.previousException`
+: :::{versionadded} 24.10.0
+  :::
+: The exception reported by the previous task attempt.
+: Since the exception is available after a failed task attempt,
+  it can only be accessed when retrying a failed task execution, and therefore when `task.attempt` is greater than 1.
+
+`task.previousTrace`
+: :::{versionadded} 24.10.0
+  :::
+: The trace record associated with the previous task attempt.
+: Since the trace record is available after a failed task attempt,
+  it can only be accessed when retrying a failed task execution, and therefore when `task.attempt` is greater than 1.
+: This is useful when retrying a task execution to access the previous task attempt runtime metrics e.g. used memory and CPUs.
+
+`task.process`
+: The current process name.
+
+`task.workDir`
+: *Available only in `exec:` blocks*
+: The task unique directory.
+
+Additionally, the [directive values](#directives) for the given task can be accessed via `task.<directive>`.
+
+(process-reference-inputs)=
+
+## Inputs
+
+`val( identifier )`
+
+: Declare a variable input. The received value can be any type, and it will be made available to the process body (i.e. `script`, `shell`, `exec`) as a variable given by `identifier`.
+
+`file( identifier | stageName )`
+
+: :::{deprecated} 19.10.0
+  Use `path` instead.
+  :::
+
+: Declare a file input. The received value can be any type, and it will be staged into the task directory. If the received value is not a file or collection of files, it is implicitly converted to a string and written to a file.
+
+: The argument can be an identifier or string. If an identifier, the received value will be made available to the process body as a variable. If a string, the received value will be staged into the task directory under the given alias.
+
+`path( identifier | stageName )`
+
+: Declare a file input. The received value can be any type, and it will be staged into the task directory. If the received value is not a file or collection of files, it is implicitly converted to a string and written to a file.
+
+: The argument can be an identifier or string. If an identifier, the received value will be made available to the process body as a variable. If a string, the received value will be staged into the task directory under the given alias.
+
+: Available options:
+
+  `arity`
+  : :::{versionadded} 23.09.0-edge
+    :::
+  : Specify the number of expected files. Can be a number, e.g. `'1'`, or a range, e.g. `'1..*'`. If a task receives an invalid number of files for this `path` input, it will fail.
+
+  `name`
+  : Specify how the file should be named in the task work directory. Can be a name or a pattern.
+
+  `stageAs`
+  : Alias of `name`.
+
+`env( name )`
+
+: Declare an environment variable input. The received value should be a string, and it will be exported to the task environment as an environment variable given by `name`.
+
+`stdin`
+
+: Declare a `stdin` input. The received value should be a string, and it will be provided as the standard input (i.e. `stdin`) to the task script. It should be declared only once for a process.
+
+`tuple( arg1, arg2, ... )`
+
+: Declare a tuple input. Each argument should be an input declaration such as `val`, `path`, `env`, or `stdin`.
+
+: The received value should be a tuple with the same number of elements as the `tuple` declaration, and each received element should be compatible with the corresponding `tuple` argument. Each tuple element is treated the same way as if it were a standalone input.
+
+(process-reference-outputs)=
+
+## Outputs
+
+`val( value )`
+
+: Declare a variable output. The argument can be any value, and it can reference any output variables defined in the process body (i.e. variables declared without the `def` keyword).
+
+`file( pattern )`
+
+: :::{deprecated} 19.10.0
+  Use `path` instead.
+  :::
+
+: Declare a file output. It receives the output files from the task environment that match the given pattern.
+
+: Multiple patterns can be specified using the colon separator (`:`). The union of all files matched by each pattern will be collected.
+
+`path( pattern, [options] )`
+
+: Declare a file output. It receives the output files from the task environment that match the given pattern.
+
+: Available options:
+
+  `arity`
+  : :::{versionadded} 23.09.0-edge
+    :::
+  : Specify the number of expected files. Can be a number or a range. If a task produces an invalid number of files for this `path` output, it will fail.
+
+  : If the arity is `1`, a single file will be emitted. Otherwise, a list will always be emitted, even if only one file is produced.
+  
+  : :::{warning}
+    If the arity is not specified, a single file or list will be emitted based on whether a single file or multiple files are produced at runtime, resulting potentially in an output channel with a mixture of files and file collections.
+    :::
+
+  `followLinks`
+  : When `true`, target files are returned in place of any matching symlink (default: `true`).
+
+  `glob`
+  : When `true`, the specified name is interpreted as a glob pattern (default: `true`).
+
+  `hidden`
+  : When `true`, hidden files are included in the matching output files (default: `false`).
+
+  `includeInputs`
+  : When `true` and the output path is a glob pattern, any input files matching the pattern are also included in the output (default: `false`).
+
+  `maxDepth`
+  : Maximum number of directory levels to visit (default: no limit).
+
+  `type`
+  : Type of paths returned, either `file`, `dir` or `any` (default: `any`, or `file` if the specified file name pattern contains a double star (`**`)).
+
+`env( name )`
+
+: Declare an environment variable output. It receives the value of the environment variable (given by `name`) from the task environment.
+
+: :::{versionchanged} 23.12.0-edge
+  Prior to this version, if the environment variable contained multiple lines of output, the output would be compressed to a single line by converting newlines to spaces.
+  :::
+
+`stdout`
+
+: Declare a `stdout` output. It receives the standard output of the task script.
+
+`eval( command )`
+
+: :::{versionadded} 24.02.0-edge
+  :::
+
+: Declare an `eval` output. It receives the standard output of the given command, which is executed in the task environment after the task script.
+
+: If the command fails, the task will also fail.
+
+`tuple( arg1, arg2, ... )`
+
+: Declare a tuple output. Each argument should be an output declaration such as `val`, `path`, `env`, `stdin`, or `eval`. Each tuple element is treated the same way as if it were a standalone output.
+
+(process-additional-options)=
+
+### Generic options
+
+The following options are available for all process outputs:
+
+`emit: <name>`
+
+: Defines the name of the output channel.
+
+`optional: true | false`
+
+: When `true`, the task will not fail if the specified output is missing (default: `false`).
+
+`topic: <name>`
+
+: :::{versionadded} 23.11.0-edge
+  :::
+
+: *Experimental: may change in a future release.*
+
+: Defines the {ref}`channel topic <channel-topic>` to which the output will be sent.
+
+(process-reference-directives)=
+
+## Directives
+
+(process-accelerator)=
+
+### accelerator
+
+:::{versionadded} 19.09.0-edge
+:::
+
+The `accelerator` directive allows you to request hardware accelerators (e.g. GPUs) for the task execution. For example:
+
+```nextflow
+process foo {
+    accelerator 4, type: 'nvidia-tesla-k80'
+
+    script:
+    """
+    your_gpu_enabled --command --line
+    """
+}
+```
+
+The above examples will request 4 GPUs of type `nvidia-tesla-k80`.
+
+:::{note}
+This directive is only used by certain executors. Refer to the {ref}`executor-page` page to see which executors support this directive.
+:::
+
+:::{note}
+Additional options may be required to fully enable the use of accelerators. When using containers with GPUs, you must pass the GPU drivers through to the container. For Docker, this requires the option `--gpus all` in the docker run command. For Apptainer/Singularity, this requires the option `--nv`. The specific implementation details depend on the accelerator and container type being used.
+:::
+
+:::{note}
+The accelerator `type` option depends on the target execution platform. Refer to the platform-specific documentation for details on the available accelerators:
+
+- [Google Cloud](https://cloud.google.com/compute/docs/gpus/)
+- [Kubernetes](https://kubernetes.io/docs/tasks/manage-gpus/scheduling-gpus/#clusters-containing-different-types-of-gpus)
+
+The accelerator `type` option is not supported for AWS Batch. You can control the accelerator type indirectly through the allowed instance types in your Compute Environment. See the [AWS Batch FAQs](https://aws.amazon.com/batch/faqs/?#GPU_Scheduling_) for more information.
+:::
+
+(process-afterscript)=
+
+### afterScript
+
+The `afterScript` directive allows you to execute a custom (Bash) snippet immediately *after* the main process has run. This may be useful to clean up your staging area.
+
+:::{note}
+When combined with the {ref}`container directive <process-container>`, the `afterScript` will be executed outside the specified container. In other words, the `afterScript` is always executed in the host environment.
+:::
+
+(process-arch)=
+
+### arch
+
+The `arch` directive allows you to define the CPU architecture to build the software in use by the process' task. For example:
+
+```nextflow
+process cpu_task {
+    spack 'blast-plus@2.13.0'
+    arch 'linux/x86_64', target: 'cascadelake'
+
+    script:
+    """
+    blastp -query input_sequence -num_threads ${task.cpus}
+    """
+}
+```
+
+The example above declares that the CPU generic architecture is `linux/x86_64` (X86 64 bit), and more specifically that the microarchitecture is `cascadelake` (a specific generation of Intel CPUs).
+
+This directive is currently used by the following Nextflow functionalities:
+
+- by the [spack](#spack) directive, to build microarchitecture-optimised applications;
+- by the {ref}`wave-page` service, to build containers for one of the generic families of CPU architectures (see below);
+- by the `spack` strategy within {ref}`wave-page`, to optimise the container builds for specific CPU microarchitectures.
+
+Allowed values for the `arch` directive are as follows, grouped by equivalent family (choices available for the sake of compatibility):
+- X86 64 bit: `linux/x86_64`, `x86_64`, `linux/amd64`, `amd64`
+- ARM 64 bit: `linux/aarch64`, `aarch64`, `linux/arm64`, `arm64`, `linux/arm64/v8`
+- ARM 64 bit, older generation: `linux/arm64/v7`
+
+Examples of values for the architecture `target` option are `cascadelake`, `icelake`, `zen2` and `zen3`. See the [Spack documentation](https://spack.readthedocs.io/en/latest/basic_usage.html#support-for-specific-microarchitectures) for the full and up-to-date list of meaningful targets.
+
+(process-array)=
+
+### array
+
+:::{versionadded} 24.04.0
+:::
+
+:::{warning} *Experimental: may change in a future release.*
+:::
+
+The `array` directive allows you to submit tasks as *job arrays* for executors that support it.
+
+A job array is a collection of jobs with the same resource requirements and the same script (parameterized by an index). Job arrays incur significantly less scheduling overhead compared to individual jobs, and as a result they are preferred by HPC schedulers where possible.
+
+The directive should be specified with a given array size, along with an executor that supports job arrays. For example:
+
+```nextflow
+process cpu_task {
+    executor 'slurm'
+    array 100
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+Nextflow currently supports job arrays for the following executors:
+
+- {ref}`awsbatch-executor`
+- {ref}`google-batch-executor`
+- {ref}`lsf-executor`
+- {ref}`pbs-executor`
+- {ref}`pbspro-executor`
+- {ref}`sge-executor`
+- {ref}`slurm-executor`
+
+A process using job arrays will collect tasks and submit each batch as a job array when it is ready. Any "leftover" tasks will be submitted as a partial job array.
+
+Once a job array is submitted, each "child" task is executed as an independent job. Any tasks that fail (and can be retried) will be retried without interfering with the tasks that succeeded. Retried tasks are submitted individually rather than through a job array, in order to allow for the use of {ref}`dynamic resources <dynamic-task-resources>`.
+
+The following directives must be uniform across all tasks in a process that uses job arrays, because these directives are specified once for the entire job array:
+
+- {ref}`process-accelerator`
+- {ref}`process-clusterOptions`
+- {ref}`process-cpus`
+- {ref}`process-disk`
+- {ref}`process-machineType`
+- {ref}`process-memory`
+- {ref}`process-queue`
+- {ref}`process-resourcelabels`
+- {ref}`process-resourcelimits`
+- {ref}`process-time`
+
+For cloud-based executors like AWS Batch, or when using Fusion with any executor, the following additional directives must be uniform:
+
+- {ref}`process-container`
+- {ref}`process-containerOptions`
+
+(process-beforescript)=
+
+### beforeScript
+
+The `beforeScript` directive allows you to execute a custom (Bash) snippet *before* the main process script is run. This may be useful to initialise the underlying cluster environment or for other custom initialisation.
+
+For example:
+
+```nextflow
+process foo {
+  beforeScript 'source /cluster/bin/setup'
+
+  script:
+  """
+  echo bar
+  """
+}
+```
+
+When the process is containerized (using the {ref}`process-container` directive), the `beforeScript` will be executed in the container only if the executor is *container-native* (e.g. cloud batch executors, Kubernetes). Otherwise, the `beforeScript` will be executed outside the container.
+
+(process-cache)=
+
+### cache
+
+The `cache` directive allows you to store the process results to a local cache. When the cache is enabled *and* the pipeline is launched with the {ref}`resume <getstarted-resume>` option, any task executions that are already cached will be re-used. See the {ref}`cache-resume-page` page for more information about how the cache works.
+
+The cache is enabled by default, but you can disable it for a specific process by setting the `cache` directive to `false`. For example:
+
+```nextflow
+process noCacheThis {
+  cache false
+  // ...
+}
+```
+
+The following options are available:
+
+`false`
+: Disable caching.
+
+`true` (default)
+: Enable caching. Input file metadata (name, size, last updated timestamp) are included in the cache keys.
+
+`'deep'`
+: Enable caching. Input file content is included in the cache keys.
+
+`'lenient'`
+: Enable caching. Minimal input file metadata (name and size only) are included in the cache keys.
+: This strategy provides a workaround for incorrect caching invalidation observed on shared file systems due to inconsistent file timestamps.
+
+(process-clusteroptions)=
+
+### clusterOptions
+
+The `clusterOptions` directive allows the usage of any native configuration option accepted by your cluster submit command. You can use it to request non-standard resources or use settings that are specific to your cluster and not supported out of the box by Nextflow.
+
+The cluster options can be a string:
+
+```nextflow
+process foo {
+  clusterOptions '-x 1 -y 2'
+  // ...
+}
+```
+
+:::{versionchanged} 24.04.0
+Prior to this version, grid executors that require each option to be on a separate line in the job script would attempt to split multiple options using a variety of different conventions. Multiple options can now be specified more clearly using a string list as shown below.
+:::
+
+The cluster options can also be a string list:
+
+```nextflow
+process foo {
+  clusterOptions '-x 1', '-y 2', '--flag'
+  // ...
+}
+```
+
+Grid executors that require one option per line will write each option to a separate line, while grid executors that allow multiple options per line will write all options to a single line, the same as with a string. This form is useful to control how the options are split across lines when it is required by the scheduler.
+
+:::{note}
+This directive is only used by grid executors. Refer to the {ref}`executor-page` page to see which executors support this directive.
+:::
+
+:::{warning}
+While you can use the `clusterOptions` directive to specify options that are supported as process directives (`queue`, `memory`, `time`, etc), you should not use both at the same time, as it will cause undefined behavior. Most HPC schedulers will either fail or simply ignore one or the other.
+:::
+
+(process-conda)=
+
+### conda
+
+The `conda` directive allows for the definition of the process dependencies using the [Conda](https://conda.io) package manager.
+
+Nextflow automatically sets up an environment for the given package names listed by in the `conda` directive. For example:
+
+```nextflow
+process foo {
+  conda 'bwa=0.7.15'
+
+  script:
+  """
+  your_command --here
+  """
+}
+```
+
+Multiple packages can be specified separating them with a blank space e.g. `bwa=0.7.15 fastqc=0.11.5`. The name of the channel from where a specific package needs to be downloaded can be specified using the usual Conda notation i.e. prefixing the package with the channel name as shown here `bioconda::bwa=0.7.15`.
+
+The `conda` directive also allows the specification of a Conda environment file path or the path of an existing environment directory. See the {ref}`conda-page` page for further details.
+
+(process-container)=
+
+### container
+
+The `container` directive allows you to execute the process script in a [Docker](http://docker.io) container.
+
+It requires the Docker daemon to be running in machine where the pipeline is executed, i.e. the local machine when using the *local* executor or the cluster nodes when the pipeline is deployed through a *grid* executor.
+
+For example:
+
+```nextflow
+process runThisInDocker {
+  container 'dockerbox:tag'
+
+  script:
+  """
+  your_command --here
+  """
+}
+```
+
+Simply replace in the above script `dockerbox:tag` with the name of the Docker image you want to use.
+
+:::{tip}
+Containers are a very useful way to execute your scripts in a reproducible self-contained environment or to run your pipeline in the cloud.
+:::
+
+:::{note}
+This directive is ignored for processes that are {ref}`executed natively <process-native>`.
+:::
+
+(process-containeroptions)=
+
+### containerOptions
+
+The `containerOptions` directive allows you to specify any container execution option supported by the underlying container engine (ie. Docker, Singularity, etc). This can be useful to provide container settings only for a specific process e.g. mount a custom path:
+
+```nextflow
+process runThisWithDocker {
+    container 'busybox:latest'
+    containerOptions '--volume /data/db:/db'
+
+    output:
+    path 'output.txt'
+
+    script:
+    """
+    your_command --data /db > output.txt
+    """
+}
+```
+
+:::{warning}
+This feature is not supported by the {ref}`k8s-executor` and {ref}`google-lifesciences-executor` executors.
+:::
+
+(process-cpus)=
+
+### cpus
+
+The `cpus` directive allows you to define the number of (logical) CPU required by the process' task. For example:
+
+```nextflow
+process big_job {
+  cpus 8
+  executor 'sge'
+
+  script:
+  """
+  blastp -query input_sequence -num_threads ${task.cpus}
+  """
+}
+```
+
+This directive is required for tasks that execute multi-process or multi-threaded commands/tools and it is meant to reserve enough CPUs when a pipeline task is executed through a cluster resource manager.
+
+See also: [penv](#penv), [memory](#memory), [time](#time), [queue](#queue), [maxForks](#maxforks)
+
+(process-debug)=
+
+### debug
+
+By default the `stdout` produced by the commands executed in all processes is ignored. By setting the `debug` directive to `true`, you can forward the process `stdout` to the current top running process `stdout` file, showing it in the shell terminal.
+
+For example:
+
+```nextflow
+process sayHello {
+  debug true
+
+  script:
+  """
+  echo Hello
+  """
+}
+```
+
+```
+Hello
+```
+
+Without specifying `debug true`, you won't see the `Hello` string printed out when executing the above example.
+
+(process-disk)=
+
+### disk
+
+The `disk` directive allows you to define how much local disk storage the process is allowed to use. For example:
+
+```nextflow
+process big_job {
+    disk '2 GB'
+    executor 'cirrus'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+The following memory unit suffix can be used when specifying the disk value:
+
+| Unit | Description |
+| ---- | ----------- |
+| B    | Bytes       |
+| KB   | Kilobytes   |
+| MB   | Megabytes   |
+| GB   | Gigabytes   |
+| TB   | Terabytes   |
+
+See {ref}`stdlib-types-memoryunit` for more information.
+
+:::{note}
+This directive is only used by certain executors. Refer to the {ref}`executor-page` page to see which executors support this directive.
+:::
+
+See also: [cpus](#cpus), [memory](#memory) [time](#time), [queue](#queue) and {ref}`dynamic-task-resources`.
+
+(process-echo)=
+
+### echo
+
+:::{deprecated} 22.04.0
+Use `debug` instead
+:::
+
+(process-error-strategy)=
+
+### errorStrategy
+
+The `errorStrategy` directive allows you to define how the process manages an error condition. By default, when an error status is returned by the executed script (i.e. when it ends with a non-zero exit status), the process stops immediately, forcing the entire pipeline to terminate.
+
+The following error strategies are available:
+
+`terminate` (default)
+: When a task fails, terminate the pipeline immediately and report an error. Pending and running jobs are killed.
+
+`finish`
+: When a task fails, wait for submitted and running tasks to finish and then terminate the pipeline, reporting an error.
+
+`ignore`
+: When a task fails, ignore it and continue the pipeline execution. If the `workflow.failOnIgnore` config option is set to `true`, the pipeline will report an error (i.e. return a non-zero exit code) upon completion. Otherwise, the pipeline will complete successfully.
+: See {ref}`stdlib-constants` for more information on `workflow.failOnIgnore`.
+
+`retry`
+: When a task fails, retry it.
+
+When setting the `errorStrategy` directive to `ignore` the process doesn't stop on an error condition, it just reports a message notifying you of the error event.
+
+For example:
+
+```nextflow
+process ignoreAnyError {
+  errorStrategy 'ignore'
+
+  // ...
+}
+```
+
+In this case, the workflow will complete successfully and return an exit status of 0. However, if you set `workflow.failOnIgnore = true` in your Nextflow configuration, the workflow will return a non-zero exit status and report the failed tasks as an error.
+
+The `retry` error strategy allows you to re-submit for execution a process returning an error condition. For example:
+
+```nextflow
+process retryIfFail {
+  errorStrategy 'retry'
+
+  // ...
+}
+```
+
+The number of times a failing process is re-executed is defined by the [maxRetries](#maxretries) and [maxErrors](#maxerrors) directives.
+
+:::{tip}
+More complex strategies depending on the task exit status or other parametric values can be defined using a dynamic `errorStrategy`. See {ref}`dynamic-directives` for details.
+:::
+
+See also: [maxErrors](#maxerrors), [maxRetries](#maxretries) and {ref}`dynamic-task-resources`.
+
+(process-executor)=
+
+### executor
+
+The `executor` defines the underlying system where processes are executed. By default a process uses the executor defined globally in the `nextflow.config` file.
+
+The `executor` directive allows you to configure what executor has to be used by the process, overriding the default configuration.
+
+The following executors are available:
+
+| Name                  | Executor                                                                                    |
+| --------------------- | ------------------------------------------------------------------------------------------- |
+| `awsbatch`            | [AWS Batch](https://aws.amazon.com/batch/) service                                          |
+| `azurebatch`          | [Azure Batch](https://azure.microsoft.com/en-us/services/batch/) service                    |
+| `condor`              | [HTCondor](https://research.cs.wisc.edu/htcondor/) job scheduler                            |
+| `google-lifesciences` | [Google Genomics Pipelines](https://cloud.google.com/life-sciences) service                 |
+| `k8s`                 | [Kubernetes](https://kubernetes.io/) cluster                                                |
+| `local`               | The computer where `Nextflow` is launched                                                   |
+| `lsf`                 | [Platform LSF](http://en.wikipedia.org/wiki/Platform_LSF) job scheduler                     |
+| `moab`                | [Moab](http://www.adaptivecomputing.com/moab-hpc-basic-edition/) job scheduler              |
+| `nqsii`               | [NQSII](https://www.rz.uni-kiel.de/en/our-portfolio/hiperf/nec-linux-cluster) job scheduler |
+| `oge`                 | Alias for the `sge` executor                                                                |
+| `pbs`                 | [PBS/Torque](http://en.wikipedia.org/wiki/Portable_Batch_System) job scheduler              |
+| `pbspro`              | [PBS Pro](https://www.pbsworks.com/) job scheduler                                          |
+| `sge`                 | Sun Grid Engine / [Open Grid Engine](http://gridscheduler.sourceforge.net/)                 |
+| `slurm`               | [SLURM](https://en.wikipedia.org/wiki/Slurm_Workload_Manager) workload manager              |
+| `uge`                 | Alias for the `sge` executor                                                                |
+
+The following example shows how to set the process's executor:
+
+```nextflow
+process doSomething {
+  executor 'sge'
+
+  // ...
+}
+```
+
+:::{note}
+Each executor supports additional directives and `executor` configuration options. See {ref}`executor-page` for more information.
+:::
+
+(process-ext)=
+
+### ext
+
+The `ext` is a special directive used as *namespace* for user custom process directives. This can be useful for advanced configuration options. For example:
+
+```nextflow
+process mapping {
+  container "biocontainers/star:${task.ext.version}"
+
+  input:
+  path genome
+  tuple val(sampleId), path(reads)
+
+  script:
+  """
+  STAR --genomeDir $genome --readFilesIn $reads ${task.ext.args ?: ''}
+  """
+}
+```
+
+In the above example, the process container version is controlled by `ext.version`, and the script supports additional command line arguments through `ext.args`.
+
+The `ext` directive can be set in the process definition:
+
+```nextflow
+process mapping {
+  ext version: '2.5.3', args: '--foo --bar'
+
+  // ...
+}
+```
+
+Or in the Nextflow configuration:
+
+```groovy
+process.ext.version = '2.5.3'
+process.ext.args = '--foo --bar'
+```
+
+(process-fair)=
+
+### fair
+
+:::{versionadded} 22.12.0-edge
+:::
+
+The `fair` directive, when enabled, guarantees that process outputs will be emitted in the order in which they were received. For example:
+
+```nextflow
+process foo {
+    fair true
+
+    input:
+    val x
+    output:
+    tuple val(task.index), val(x)
+
+    script:
+    """
+    sleep \$((RANDOM % 3))
+    """
+}
+
+workflow {
+    channel.of('A','B','C','D') | foo | view
+}
+```
+
+The above example produces:
+
+```
+[1, A]
+[2, B]
+[3, C]
+[4, D]
+```
+
+(process-label)=
+
+### label
+
+The `label` directive allows the annotation of processes with mnemonic identifier of your choice. For example:
+
+```nextflow
+process bigTask {
+  label 'big_mem'
+
+  script:
+  """
+  your_command --here
+  """
+}
+```
+
+The same label can be applied to more than a process and multiple labels can be applied to the same process using the `label` directive more than one time.
+
+:::{note}
+A label must consist of alphanumeric characters or `_`, must start with an alphabetic character and must end with an alphanumeric character.
+:::
+
+Labels are useful to organize workflow processes in separate groups which can be referenced in the configuration file to select and configure a subset of processes having similar computing requirements. See {ref}`config-process-selectors` for more information.
+
+See also: [resourceLabels](#resourcelabels)
+
+(process-machinetype)=
+
+### machineType
+
+:::{versionadded} 19.07.0
+:::
+
+The `machineType` can be used to specify a predefined Google Compute Platform [machine type](https://cloud.google.com/compute/docs/machine-types) when running using the {ref}`Google Batch <google-batch-executor>` or {ref}`Google Life Sciences <google-lifesciences-executor>` executor, or when using the autopools feature of the {ref}`Azure Batch executor<azurebatch-executor>`.
+
+This directive is optional and if specified overrides the cpus and memory directives:
+
+```nextflow
+process foo {
+  machineType 'n1-highmem-8'
+
+  script:
+  """
+  your_command --here
+  """
+}
+```
+
+See also: [cpus](#cpus) and [memory](#memory).
+
+(process-maxsubmitawait)=
+
+### maxSubmitAwait
+
+The `maxSubmitAwait` directive allows you to specify how long a task can remain in submission queue without being executed.
+Elapsed this time the task execution will fail.
+
+When used along with `retry` error strategy, it can be useful to re-schedule the task to a difference queue or
+resource requirement. For example:
+
+```nextflow
+process foo {
+  errorStrategy 'retry'
+  maxSubmitAwait '10 mins'
+  maxRetries 3
+  queue "${task.submitAttempt==1 : 'spot-compute' : 'on-demand-compute'}"
+
+  script:
+  """
+  your_command --here
+  """
+}
+```
+
+In the above example the task is submitted to the `spot-compute` on the first attempt (`task.submitAttempt==1`). If the
+task execution does not start in the 10 minutes, a failure is reported and a new submission is attempted using the
+queue named `on-demand-compute`.
+
+(process-maxerrors)=
+
+### maxErrors
+
+The `maxErrors` directive allows you to specify the maximum number of times a process can fail when using the `retry` error strategy. By default this directive is disabled, you can set it as shown in the example below:
+
+```nextflow
+process retryIfFail {
+  errorStrategy 'retry'
+  maxErrors 5
+
+  script:
+  """
+  echo 'do this as that .. '
+  """
+}
+```
+
+:::{note}
+This setting considers the **total** errors accumulated for a given process, across all instances. If you want to control the number of times a process **instance** (aka task) can fail, use `maxRetries`.
+:::
+
+See also: [errorStrategy](#errorstrategy) and [maxRetries](#maxretries).
+
+(process-maxforks)=
+
+### maxForks
+
+The `maxForks` directive allows you to define the maximum number of process instances that can be executed in parallel. By default this value is equals to the number of CPU cores available minus 1.
+
+If you want to execute a process in a sequential manner, set this directive to one. For example:
+
+```nextflow
+process doNotParallelizeIt {
+  maxForks 1
+
+  script:
+  """
+  your_command --here
+  """
+}
+```
+
+(process-maxretries)=
+
+### maxRetries
+
+The `maxRetries` directive allows you to define the maximum number of times a process instance can be re-submitted in case of failure. This value is applied only when using the `retry` error strategy. By default only one retry is allowed, you can increase this value as shown below:
+
+```nextflow
+process retryIfFail {
+    errorStrategy 'retry'
+    maxRetries 3
+
+    script:
+    """
+    echo 'do this as that .. '
+    """
+}
+```
+
+:::{note}
+There is a subtle but important difference between `maxRetries` and the `maxErrors` directive. The latter defines the total number of errors that are allowed during the process execution (the same process can launch different execution instances), while the `maxRetries` defines the maximum number of times the same process execution can be retried in case of an error.
+:::
+
+See also: [errorStrategy](#errorstrategy) and [maxErrors](#maxerrors).
+
+(process-memory)=
+
+### memory
+
+The `memory` directive allows you to define how much memory the process is allowed to use. For example:
+
+```nextflow
+process big_job {
+    memory '2 GB'
+    executor 'sge'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+The following memory unit suffix can be used when specifying the memory value:
+
+| Unit | Description |
+| ---- | ----------- |
+| B    | Bytes       |
+| KB   | Kilobytes   |
+| MB   | Megabytes   |
+| GB   | Gigabytes   |
+| TB   | Terabytes   |
+
+See {ref}`stdlib-types-memoryunit` for more information.
+
+See also: [cpus](#cpus), [time](#time), [queue](#queue) and {ref}`dynamic-task-resources`.
+
+(process-module)=
+
+### module
+
+[Environment Modules](http://modules.sourceforge.net/) is a package manager that allows you to dynamically configure your execution environment and easily switch between multiple versions of the same software tool.
+
+If it is available in your system you can use it with Nextflow in order to configure the processes execution environment in your pipeline.
+
+In a process definition you can use the `module` directive to load a specific module version to be used in the process execution environment. For example:
+
+```nextflow
+process basicExample {
+  module 'ncbi-blast/2.2.27'
+
+  script:
+  """
+  blastp -query <etc..>
+  """
+}
+```
+
+You can repeat the `module` directive for each module you need to load. Alternatively multiple modules can be specified in a single `module` directive by separating all the module names by using a `:` (colon) character as shown below:
+
+```nextflow
+process manyModules {
+  module 'ncbi-blast/2.2.27:t_coffee/10.0:clustalw/2.1'
+
+  script:
+  """
+  blastp -query <etc..>
+  """
+}
+```
+
+(process-penv)=
+
+### penv
+
+The `penv` directive allows you to define the parallel environment to be used when submitting a parallel task to the {ref}`SGE <sge-executor>` resource manager. For example:
+
+```nextflow
+process big_job {
+  cpus 4
+  penv 'smp'
+  executor 'sge'
+
+  script:
+  """
+  blastp -query input_sequence -num_threads ${task.cpus}
+  """
+}
+```
+
+This configuration depends on the parallel environment provided by your grid engine installation. Refer to your cluster documentation or contact your admin to learn more about this.
+
+See also: [cpus](#cpus), [memory](#memory), [time](#time)
+
+(process-pod)=
+
+### pod
+
+The `pod` directive allows the definition of pod specific settings, such as environment variables, secrets, and config maps, when using the {ref}`k8s-executor` executor.
+
+For example:
+
+```nextflow
+process your_task {
+  pod env: 'FOO', value: 'bar'
+
+  script:
+  """
+  echo $FOO
+  """
+}
+```
+
+The above snippet defines an environment variable named `FOO` whose value is `bar`.
+
+When defined in the Nextflow configuration file, a pod setting can be defined as a map:
+
+```groovy
+process {
+  pod = [env: 'FOO', value: 'bar']
+}
+```
+
+Or as a list of maps:
+
+```groovy
+process {
+  pod = [
+    [env: 'FOO', value: 'bar'],
+    [secret: 'my-secret/key1', mountPath: '/etc/file.txt']
+  ]
+}
+```
+
+The following options are available:
+
+`affinity: <config>`
+: :::{versionadded} 22.01.0-edge
+  :::
+: Specifies the pod [affinity](https://kubernetes.io/docs/concepts/scheduling-eviction/assign-pod-node/#affinity-and-anti-affinity) with the given configuration.
+
+`annotation: '<name>', value: '<value>'`
+: *Can be specified multiple times*
+: Defines a pod [annotation](https://kubernetes.io/docs/concepts/overview/working-with-objects/annotations/) with the given name and value.
+
+`automountServiceAccountToken: true | false`
+: :::{versionadded} 22.01.0-edge
+  :::
+: Specifies whether to [automount service account token](https://kubernetes.io/docs/tasks/configure-pod-container/configure-service-account/#opt-out-of-api-credential-automounting) into the pod (default: `true`).
+
+`config: '<configMap>/<key>', mountPath: '</absolute/path>'`
+: *Can be specified multiple times*
+: Mounts a [ConfigMap](https://kubernetes.io/docs/tasks/configure-pod-container/configure-pod-configmap/) with name and optional key to the given path. If the key is omitted, the path is interpreted as a directory and all entries in the `ConfigMap` are exposed in that path.
+
+`csi: '<config>', mountPath: '</absolute/path>'`
+: :::{versionadded} 22.11.0-edge
+  :::
+: *Can be specified multiple times*
+: Mounts a [CSI ephemeral volume](https://kubernetes.io/docs/concepts/storage/ephemeral-volumes/#csi-ephemeral-volumes) with the given configuration to the given path.
+
+`emptyDir: <config>, mountPath: '</absolute/path>'`
+: :::{versionadded} 22.11.0-edge
+  :::
+: *Can be specified multiple times*
+: Mounts an [emptyDir](https://kubernetes.io/docs/concepts/storage/volumes/#emptydir) with the given configuration to the given path.
+
+`env: '<name>', config: '<configMap>/<key>'`
+: *Can be specified multiple times*
+: Defines an environment variable whose value is defined by the given [ConfigMap](https://kubernetes.io/docs/tasks/configure-pod-container/configure-pod-configmap/) and key.
+
+`env: '<name>', fieldPath: '<fieldPath>'`
+: :::{versionadded} 21.09.1-edge
+  :::
+: *Can be specified multiple times*
+: Defines an environment variable whose value is defined by the given [field path](https://kubernetes.io/docs/tasks/inject-data-application/environment-variable-expose-pod-information/#use-pod-fields-as-values-for-environment-variables) value.
+
+: For example, the following pod option:
+
+  ```groovy
+  pod = [env: 'MY_NODE_NAME', fieldPath: 'spec.nodeName']
+  ```
+
+  Maps to the following pod spec:
+
+  ```yaml
+  env:
+    - name: MY_NODE_NAME
+      valueFrom:
+        fieldRef:
+          fieldPath: spec.nodeName
+  ```
+
+`env: '<name>', secret: '<secret>/<key>'`
+: *Can be specified multiple times*
+: Defines an environment variable whose value is defined by the given [Secret](https://kubernetes.io/docs/concepts/configuration/secret/) and key.
+
+`env: '<name>', value: '<value>'`
+: *Can be specified multiple times*
+: Defines an environment variable with the given name and value.
+
+`hostPath: '/host/absolute/path', mountPath: '</pod/absolute/path>'`
+: :::{versionadded} 23.10.0
+  :::
+: *Can be specified multiple times*
+: Allows creating [hostPath](https://kubernetes.io/docs/concepts/storage/volumes/#hostpath) volume and access it with the specified `mountPath` in the pod.
+
+`imagePullPolicy: 'IfNotPresent' | 'Always' | 'Never'`
+: Specifies the [image pull policy](https://kubernetes.io/docs/concepts/containers/images/#image-pull-policy) used by the pod to pull the container image.
+
+`imagePullSecret: '<name>'`
+: Specifies the [image pull secret](https://kubernetes.io/docs/concepts/containers/images/#specifying-imagepullsecrets-on-a-pod) used to access a private container image registry.
+
+`label: '<name>', value: '<value>'`
+: *Can be specified multiple times*
+: Defines a pod [label](https://kubernetes.io/docs/concepts/overview/working-with-objects/labels/) with the given name and value.
+
+`nodeSelector: <config>`
+: Specifies the [node selector](https://kubernetes.io/docs/concepts/scheduling-eviction/assign-pod-node/#nodeselector) with the given configuration.
+
+: The configuration can be a map or a string:
+
+  ```groovy
+  // map
+  pod = [nodeSelector: [disktype: 'ssd', cpu: 'intel']]
+
+  // string
+  pod = [nodeSelector: 'disktype=ssd,cpu=intel']
+  ```
+
+`priorityClassName: '<name>'`
+: :::{versionadded} 22.01.0-edge
+  :::
+: Specifies the [priority class name](https://kubernetes.io/docs/concepts/scheduling-eviction/pod-priority-preemption/) for pods.
+
+`privileged: true | false`
+: :::{versionadded} 22.05.0-edge
+  :::
+: Specifies whether the pod should run as a *privileged* container (default: `false`).
+
+`runAsUser: '<uid>'`
+: Specifies the user ID with which to run the container. Shortcut for the `securityContext` option.
+
+`schedulerName: '<name>'`
+: Specifies which [scheduler](https://kubernetes.io/docs/tasks/extend-kubernetes/configure-multiple-schedulers/#specify-schedulers-for-pods) is used to schedule the container.
+
+`secret: '<secret>/<key>', mountPath: '</absolute/path>'`
+: *Can be specified multiple times*
+: Mounts a [Secret](https://kubernetes.io/docs/concepts/configuration/secret/) with name and optional key to the given path. If the key is omitted, the path is interpreted as a directory and all entries in the `Secret` are exposed in that path.
+
+`securityContext: <config>`
+: Specifies the pod [security context](https://kubernetes.io/docs/tasks/configure-pod-container/security-context/) with the given configuration.
+
+`toleration: <config>`
+: :::{versionadded} 22.04.0
+  :::
+: *Can be specified multiple times*
+: Specifies the pod [toleration](https://kubernetes.io/docs/concepts/scheduling-eviction/taint-and-toleration/) with the given configuration.
+
+: The configuration should be a map corresponding to a single toleration rule. For example, the following pod options:
+
+  ```groovy
+  pod = [
+      [toleration: [key: 'key1', operator: 'Equal', value: 'value1', effect: 'NoSchedule']],
+      [toleration: [key: 'key1', operator: 'Exists', effect: 'NoSchedule']],
+  ]
+  ```
+
+  Maps to the following pod spec:
+
+  ```yaml
+  tolerations:
+    - key: "key1"
+      operator: "Equal"
+      value: "value1"
+      effect: "NoSchedule"
+    - key: "key1"
+      operator: "Exists"
+      effect: "NoSchedule"
+  ```
+
+`ttlSecondsAfterFinished`
+: :::{versionadded} 24.02.0-edge
+  :::
+: Specifies the [TTL mechanism](https://kubernetes.io/docs/concepts/workloads/controllers/job/#ttl-mechanism-for-finished-jobs) for finished jobs in seconds. Applies to both successful and failed jobs.
+
+`volumeClaim: '<name>', mountPath: '</absolute/path>' [, subPath: '<path>', readOnly: true | false]`
+: *Can be specified multiple times*
+: Mounts a [Persistent volume claim](https://kubernetes.io/docs/concepts/storage/persistent-volumes/) with the given name to the given path.
+: The `subPath` option can be used to mount a sub-directory of the volume instead of its root.
+: The `readOnly` option can be used to mount the volume as read-only (default: `false`)
+
+(process-publishdir)=
+
+### publishDir
+
+The `publishDir` directive allows you to publish the process output files to a specified folder. For example:
+
+```nextflow
+process foo {
+    publishDir '/data/chunks'
+
+    output:
+    path 'chunk_*'
+
+    script:
+    """
+    printf 'Hola' | split -b 1 - chunk_
+    """
+}
+```
+
+The above example splits the string `Hola` into file chunks of a single byte. When complete the `chunk_*` output files are published into the `/data/chunks` folder.
+
+:::{note}
+Only files that match the declaration in the `output` block are published, not all the outputs of the process.
+:::
+
+:::{tip}
+The `publishDir` directive can be specified more than once in order to publish output files to different target directories based on different rules.
+:::
+
+By default files are published to the target folder creating a *symbolic link* for each process output that links the file produced into the process working directory. This behavior can be modified using the `mode` option, for example:
+
+```nextflow
+process foo {
+    publishDir '/data/chunks', mode: 'copy', overwrite: false
+
+    output:
+    path 'chunk_*'
+
+    script:
+    """
+    printf 'Hola' | split -b 1 - chunk_
+    """
+}
+```
+
+:::{warning}
+Files are copied into the specified directory in an *asynchronous* manner, so they may not be immediately available in the publish directory at the end of the process execution. For this reason, downstream processes should not try to access output files through the publish directory, but through channels.
+:::
+
+Available options:
+
+`contentType`
+: :::{versionadded} 22.10.0
+  :::
+: *Experimental: currently only supported for S3.*
+: Allow specifying the media content type of the published file a.k.a. [MIME type](https://developer.mozilla.org/en-US/docs/Web/HTTP/Basics_of_HTTP/MIME_Types). If set to `true`, the content type is inferred from the file extension (default: `false`).
+
+`enabled`
+: Enable or disable the publish rule depending on the boolean value specified (default: `true`).
+
+`failOnError`
+: :::{versionchanged} 24.03.0-edge
+  The default value was changed from `false` to `true`
+  :::
+: When `true` abort the execution if some file can't be published to the specified target directory or bucket for any cause (default: `true`)
+
+`mode`
+: The file publishing method. Can be one of the following values:
+
+  - `'copy'`: Copies the output files into the publish directory.
+  - `'copyNoFollow'`: Copies the output files into the publish directory without following symlinks ie. copies the links themselves.
+  - `'link'`: Creates a hard link in the publish directory for each output file.
+  - `'move'`: Moves the output files into the publish directory. **Note**: this is only supposed to be used for a *terminal* process i.e. a process whose output is not consumed by any other downstream process.
+  - `'rellink'`: Creates a relative symbolic link in the publish directory for each output file.
+  - `'symlink'`: Creates an absolute symbolic link in the publish directory for each output file (default).
+
+`overwrite`
+: When `true` any existing file in the specified folder will be overridden (default: `true` during normal pipeline execution and `false` when pipeline execution is `resumed`).
+
+`path`
+: Specifies the directory where files need to be published. **Note**: the syntax `publishDir '/some/dir'` is a shortcut for `publishDir path: '/some/dir'`.
+
+`pattern`
+: Specifies a [glob][glob] file pattern that selects which files to publish from the overall set of output files.
+
+`saveAs`
+: A closure which, given the name of the file being published, returns the actual file name or a full path where the file is required to be stored. This can be used to rename or change the destination directory of the published files dynamically by using a custom strategy. Return the value `null` from the closure to *not* publish a file. This is useful when the process has multiple output files, but you want to publish only some of them.
+
+`storageClass`
+: :::{versionadded} 22.12.0-edge
+  :::
+: *Experimental: currently only supported for S3.*
+: Allow specifying the storage class to be used for the published file.
+
+`tags`
+: :::{versionadded} 21.12.0-edge
+  :::
+: *Experimental: currently only supported for S3.*
+: Allow the association of arbitrary tags with the published file e.g. `tags: [FOO: 'Hello world']`.
+
+(process-queue)=
+
+### queue
+
+The `queue` directive allows you to set the `queue` where jobs are scheduled when using a grid based executor in your pipeline. For example:
+
+```nextflow
+process grid_job {
+    queue 'long'
+    executor 'sge'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+:::{tip}
+Some grid executors support multiple queue names as a comma-separated list:
+
+```nextflow
+queue 'short,long,cn-el6'
+```
+
+However, this does not generally apply to other executors such as AWS Batch, Azure Batch, Google Batch.
+:::
+
+:::{note}
+This directive is only used by certain executors. Refer to the {ref}`executor-page` page to see which executors support this directive.
+:::
+
+(process-resourcelabels)=
+
+### resourceLabels
+
+:::{versionadded} 22.09.1-edge
+:::
+
+The `resourceLabels` directive allows you to specify custom name-value pairs that Nextflow applies to the computing resource used to carry out the process execution. Resource labels can be specified using the syntax shown below:
+
+```nextflow
+process my_task {
+    resourceLabels region: 'some-region', user: 'some-username'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+The limits and the syntax of the corresponding cloud provider should be taken into consideration when using resource labels.
+
+Resource labels are currently supported by the following executors:
+
+- {ref}`awsbatch-executor`
+- {ref}`azurebatch-executor`
+- {ref}`google-batch-executor`
+- {ref}`google-lifesciences-executor`
+- {ref}`k8s-executor`
+
+:::{versionadded} 23.09.0-edge
+Resource labels are supported for Azure Batch when using automatic pool creation.
+
+Resource labels in Azure are added to pools, rather than jobs, in order to facilitate cost analysis. A new pool will be created for each new set of resource labels, therefore it is recommended to also set `azure.batch.deletePoolsOnCompletion = true` when using process-specific resource labels.
+:::
+
+See also: [label](#label)
+
+(process-resourcelimits)=
+
+### resourceLimits
+
+:::{versionadded} 24.04.0
+:::
+
+The `resourceLimits` directive allows you to specify environment-specific limits for task resource requests. Resource limits can be specified in a process as follows:
+
+```nextflow
+process my_task {
+  resourceLimits cpus: 24, memory: 768.GB, time: 72.h
+
+  script:
+  """
+  your_command --here
+  """
+}
+```
+
+Or in the Nextflow configuration:
+
+```nextflow
+process {
+    resourceLimits = [ cpus: 24, memory: 768.GB, time: 72.h ]
+}
+```
+
+Resource limits can be defined for the following directives:
+
+- [cpus](#cpus)
+- [disk](#disk)
+- [memory](#memory)
+- [time](#time)
+
+Resource limits are a useful way to specify environment-specific limits alongside tasks with {ref}`dynamic resources <dynamic-task-resources>`. Normally, if a task requests more resources than can be provisioned (e.g. a task requests 32 cores but the largest node in the cluster has 24), the task will either fail or cause the pipeline to hang forever as it will never be scheduled. If the `resourceLimits` directive is defined with these limits, the task resources will be automatically reduced to comply with these limits before the job is submitted.
+
+(process-scratch)=
+
+### scratch
+
+The `scratch` directive allows you to execute the process in a temporary folder that is local to the execution node.
+
+This is useful when your pipeline is launched by using a grid executor, because it allows you to decrease the NFS overhead by running the pipeline processes in a temporary directory in the local disk of the actual execution node. Only the files declared as output in the process definition will be copied in the pipeline working area.
+
+In its basic form simply specify `true` at the directive value, as shown below:
+
+```nextflow
+process simpleTask {
+  scratch true
+
+  output:
+  path 'data_out'
+
+  script:
+  """
+  your_command --here
+  """
+}
+```
+
+By doing this, it tries to execute the script in the directory defined by the variable `$TMPDIR` in the execution node. If this variable does not exist, it will create a new temporary directory by using the Linux command `mktemp`.
+
+:::{note}
+Cloud-based executors use `scratch = true` by default, since the work directory resides in object storage.
+:::
+
+The following values are supported:
+
+`false`
+: Do not use a scratch directory.
+
+`true`
+: Create a scratch directory in the directory defined by the `$TMPDIR` environment variable, or `$(mktemp /tmp)` if `$TMPDIR` is not set.
+
+`'$YOUR_VAR'`
+: Create a scratch directory in the directory defined by the given environment variable, or `$(mktemp /tmp)` if that variable is not set. The value must use single quotes, otherwise the environment variable will be evaluated in the pipeline script context.
+
+`'/my/tmp/path'`
+: Create a scratch directory in the specified directory.
+
+`'ram-disk'`
+: Create a scratch directory in the RAM disk `/dev/shm/`.
+
+(process-directive-shell)=
+
+### shell
+
+The `shell` directive allows you to define a custom shell command for process scripts. By default, script blocks are executed with `/bin/bash -ue`.
+
+```nextflow
+process doMoreThings {
+    shell '/bin/bash', '-euo', 'pipefail'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+The same directive could be specified in your Nextflow configuration as follows:
+
+```groovy
+process.shell = ['/bin/bash', '-euo', 'pipefail']
+```
+
+(process-spack)=
+
+### spack
+
+The `spack` directive allows for the definition of the process dependencies using the [Spack](https://spack.io) package manager.
+
+Nextflow automatically sets up an environment for the given package names listed by in the `spack` directive. For example:
+
+```nextflow
+process foo {
+    spack 'bwa@0.7.15'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+Multiple packages can be specified separating them with a blank space, e.g. `bwa@0.7.15 fastqc@0.11.5`.
+
+The `spack` directive also allows the specification of a Spack environment file path or the path of an existing environment directory. See the {ref}`spack-page` page for further details.
+
+(process-stageinmode)=
+
+### stageInMode
+
+The `stageInMode` directive defines how input files are staged into the process work directory. The following values are allowed:
+
+`'copy'`
+: Input files are staged in the process work directory by creating a copy.
+
+`'link'`
+: Input files are staged in the process work directory by creating a hard link for each of them.
+
+`'rellink'`
+: Input files are staged in the process work directory by creating a symbolic link with a relative path for each of them.
+
+`'symlink'`
+: Input files are staged in the process work directory by creating a symbolic link with an absolute path for each of them (default).
+
+(process-stageoutmode)=
+
+### stageOutMode
+
+The `stageOutMode` directive defines how output files are staged out from the scratch directory to the process work directory. The following values are allowed:
+
+`'copy'`
+: Output files are copied from the scratch directory to the work directory.
+
+`'fcp'`
+: :::{versionadded} 23.02.0-edge
+  :::
+: Output files are copied from the scratch directory to the work directory by using the [fcp](https://github.com/Svetlitski/fcp) utility (note: it must be available in your cluster computing nodes).
+
+`'move'`
+: Output files are moved from the scratch directory to the work directory.
+
+`'rclone'`
+: :::{versionadded} 23.01.0-edge
+  :::
+: Output files are copied from the scratch directory to the work directory by using the [rclone](https://rclone.org) utility (note: it must be available in your cluster computing nodes).
+
+`'rsync'`
+: Output files are copied from the scratch directory to the work directory by using the `rsync` utility.
+
+See also: [scratch](#scratch).
+
+(process-storedir)=
+
+### storeDir
+
+The `storeDir` directive allows you to define a directory that is used as a *permanent* cache for your process results.
+
+In more detail, it affects the process execution in two main ways:
+
+1. The process is executed only if the files declared in the `output` block do not exist in the directory specified by the `storeDir` directive. When the files exist the process execution is skipped and these files are used as the actual process result.
+2. Whenever a process is successfully completed the files listed in the `output` block are moved into the directory specified by the `storeDir` directive.
+
+The following example shows how to use the `storeDir` directive to create a directory containing a BLAST database for each species specified by an input parameter:
+
+```nextflow
+process formatBlastDatabases {
+  storeDir '/db/genomes'
+
+  input:
+  path species
+
+  output:
+  path "${dbName}.*"
+
+  script:
+  dbName = species.baseName
+  """
+  makeblastdb -dbtype nucl -in ${species} -out ${dbName}
+  """
+}
+```
+
+:::{warning}
+The `storeDir` directive is meant for long-term process caching and should not be used to publish output files or organize outputs into a semantic directory structure. In those cases, use the [publishDir](#publishdir) directive instead.
+:::
+
+:::{note}
+The use of AWS S3 paths is supported, however it requires the installation of the [AWS CLI](https://aws.amazon.com/cli/) (i.e. `aws`) in the target compute node.
+:::
+
+(process-tag)=
+
+### tag
+
+The `tag` directive allows you to associate each process execution with a custom label, so that it will be easier to identify them in the log file or in the trace execution report. For example:
+
+```nextflow
+process foo {
+  tag "$code"
+
+  input:
+  val code
+
+  script:
+  """
+  echo $code
+  """
+}
+
+workflow {
+  Channel.of('alpha', 'gamma', 'omega') | foo
+}
+```
+
+The above snippet will print a log similar to the following one, where process names contain the tag value:
+
+```
+[6e/28919b] Submitted process > foo (alpha)
+[d2/1c6175] Submitted process > foo (gamma)
+[1c/3ef220] Submitted process > foo (omega)
+```
+
+See also {ref}`Trace execution report <trace-report>`
+
+(process-time)=
+
+### time
+
+The `time` directive allows you to define how long a process is allowed to run. For example:
+
+```nextflow
+process big_job {
+    time '1h'
+
+    script:
+    """
+    your_command --here
+    """
+}
+```
+
+The following time unit suffixes can be used when specifying the duration value:
+
+| Unit                            | Description  |
+| ------------------------------- | ------------ |
+| `ms`, `milli`, `millis`         | Milliseconds |
+| `s`, `sec`, `second`, `seconds` | Seconds      |
+| `m`, `min`, `minute`, `minutes` | Minutes      |
+| `h`, `hour`, `hours`            | Hours        |
+| `d`, `day`, `days`              | Days         |
+
+Multiple units can be used in a single declaration, for example: `'1day 6hours 3minutes 30seconds'`
+
+See {ref}`stdlib-types-duration` for more information.
+
+:::{note}
+This directive is only used by certain executors. Refer to the {ref}`executor-page` page to see which executors support this directive.
+:::
+
+See also: [cpus](#cpus), [memory](#memory), [queue](#queue) and {ref}`dynamic-task-resources`.
diff --git a/docs/reference/stdlib.md b/docs/reference/stdlib.md
new file mode 100644
index 0000000000..633e51b0eb
--- /dev/null
+++ b/docs/reference/stdlib.md
@@ -0,0 +1,699 @@
+(stdlib-page)=
+
+# Standard library
+
+This page describes the built-in constants, functions, and types provided by Nextflow.
+
+## Globals
+
+(stdlib-constants)=
+
+### Constants
+
+The following constants are globally available in a Nextflow script:
+
+`baseDir`
+: :::{deprecated} 20.04.0
+  :::
+: Alias of `workflow.projectDir`.
+
+`launchDir`
+: Alias of `workflow.launchDir`.
+
+`moduleDir`
+: The directory where a module script is located (equivalent to `projectDir` if used in the main script).
+
+`nextflow`
+: Map of Nextflow runtime information.
+
+  `nextflow.build`
+  : Nextflow runtime build number.
+
+  `nextflow.timestamp`
+  : Nextflow runtime compile timestamp.
+
+  `nextflow.version`
+  : Nextflow runtime version number.
+
+  `nextflow.version.matches()`
+  : Check whether the Nextflow runtime satisfies a version requirement.
+
+  : The version requirement string can be prefixed with the usual comparison operators:
+    - `=` or `==`: equal to
+    - `<` (`<=`): less than (or equal to)
+    - `>` (`>=`): greater than (or equal to)
+    - `!=` or `<>`: not equal
+
+    For example:
+
+    ```nextflow
+    if( !nextflow.version.matches('>=23.10') ) {
+        error "This workflow requires Nextflow version 23.10 or greater -- You are running version $nextflow.version"
+    }
+    ```
+
+  : Alternatively, the version can be postfixed with `+`, which is similar to `==` but also allows the last version part to be greater. For example, `23.10.1+` is satisfied by `23.10.1` and `23.10.2`, but not `23.11.x` or `23.09.x`. Additionally, `23.10.+` is equivalent to `23.10.0+`. This operator is a useful way to enforce a specific version while allowing for newer patch releases.
+
+`params`
+: Map of workflow parameters specified in the config file or as command line options.
+
+`projectDir`
+: Alias of `workflow.projectDir`.
+
+`secrets`
+: :::{versionadded} 24.02.0-edge
+  :::
+: Dictionary like object holding workflow secrets. Read the {ref}`secrets-page` page for more information.
+
+`workDir`
+: Alias of `workflow.workDir`.
+
+`workflow`
+: Map of workflow runtime information.
+
+  `workflow.commandLine`
+  : Command line as entered by the user to launch the workflow execution.
+
+  `workflow.commitId`
+  : Git commit ID of the executed workflow repository.
+  : When providing a Git tag, branch name, or commit hash using the `-r` CLI option, the associated `workflow.commitId` is also populated.
+
+  `workflow.complete`
+  : *Available only in the `workflow.onComplete` handler*
+  : Timestamp of workflow when execution is completed.
+
+  `workflow.configFiles`
+  : Configuration files used for the workflow execution.
+
+  `workflow.container`
+  : Docker image used to run workflow tasks. When more than one image is used it returns a map object containing `[process name, image name]` pair entries.
+
+  `workflow.containerEngine`
+  : Returns the name of the container engine (e.g. docker or singularity) or null if no container engine is enabled.
+
+  `workflow.duration`
+  : *Available only in the `workflow.onComplete` handler*
+  : Time elapsed to complete workflow execution.
+
+  `workflow.errorMessage`
+  : *Available only in the `workflow.onComplete` and `workflow.onError` handlers*
+  : Error message of the task that caused the workflow execution to fail.
+
+  `workflow.errorReport`
+  : *Available only in the `workflow.onComplete` and `workflow.onError` handlers*
+  : Detailed error of the task that caused the workflow execution to fail.
+
+  `workflow.exitStatus`
+  : *Available only in the `workflow.onComplete` and `workflow.onError` handlers*
+  : Exit status of the task that caused the workflow execution to fail.
+
+  `workflow.failOnIgnore`
+  : :::{versionadded} 24.05.0-edge
+    :::
+  : Whether the `workflow.failOnIgnore` config option was enabled.
+  : See also: {ref}`process-error-strategy`
+
+  `workflow.fusion.enabled`
+  : Whether Fusion is enabled.
+
+  `workflow.fusion.version`
+  : Fusion version in use.
+
+  `workflow.homeDir`
+  : User system home directory.
+
+  `workflow.launchDir`
+  : Directory where the workflow was launched.
+
+  `workflow.manifest`
+  : Entries of the workflow manifest.
+
+  `workflow.outputDir`
+  : :::{versionadded} 24.10.0
+    :::
+  : Workflow output directory.
+
+  `workflow.preview`
+  : :::{versionadded} 24.04.0
+    :::
+  : Whether the current workflow run is a preview run.
+
+  `workflow.profile`
+  : Used configuration profile.
+
+  `workflow.projectDir`
+  : Directory where the workflow project is located.
+
+  `workflow.repository`
+  : Project repository Git remote URL.
+
+  `workflow.resume`
+  : Returns `true` whenever the current instance is resumed from a previous execution.
+
+  `workflow.revision`
+  : Git branch/tag of the executed workflow repository.
+  : When providing a Git tag or branch name using the `-r` CLI option, the `workflow.revision` is also populated.
+
+  `workflow.runName`
+  : Mnemonic name assigned to this execution instance.
+
+  `workflow.scriptFile`
+  : Project main script file path.
+
+  `workflow.scriptId`
+  : Project main script unique hash ID.
+
+  `workflow.scriptName`
+  : Project main script file name.
+
+  `workflow.sessionId`
+  : Unique identifier (UUID) associated to current execution.
+
+  `workflow.start`
+  : Timestamp of workflow at execution start.
+
+  `workflow.stubRun`
+  : Returns `true` whenever the current instance is a stub-run execution .
+
+  `workflow.success`
+  : *Available only in the `workflow.onComplete` and `workflow.onError` handlers*
+  : Reports if the execution completed successfully.
+
+  `workflow.userName`
+  : User system account name.
+
+  `workflow.wave.enabled`
+  : Whether Wave is enabled.
+
+  `workflow.workDir`
+  : The directory where task temporary files are stored.
+
+(stdlib-functions)=
+
+### Functions
+
+The following functions are available in Nextflow scripts:
+
+`branchCriteria( closure )`
+: Create a branch criteria to use with the {ref}`operator-branch` operator.
+
+`env( name )`
+: :::{versionadded} 24.11.0-edge
+  :::
+: Get the value of the environment variable with the specified name in the Nextflow launch environment.
+
+`error( message = null )`
+: Throw a script runtime error with an optional error message.
+
+`exit( exitCode = 0, message = null )`
+: :::{deprecated} 22.06.0-edge
+  Use `error()` instead
+  :::
+: Stop the pipeline execution and return an exit code and optional error message.
+
+`file( filePattern, [options] )`
+: Get one or more files from a path or glob pattern. Returns a [Path](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/file/Path.html) or list of Paths if there are multiple files.
+
+: The following options are available:
+
+  `checkIfExists`
+  : When `true`, throws an exception if the specified path does not exist in the file system (default: `false`)
+
+  `followLinks`
+  : When `true`, follows symbolic links when traversing a directory tree, otherwise treats them as files (default: `true`)
+
+  `glob`
+  : When `true`, interprets characters `*`, `?`, `[]` and `{}` as glob wildcards, otherwise handles them as normal characters (default: `true`)
+
+  `hidden`
+  : When `true`, includes hidden files in the resulting paths (default: `false`)
+
+  `maxDepth`
+  : Maximum number of directory levels to visit (default: *no limit*)
+
+  `type`
+  : Type of paths returned, can be `'file'`, `'dir'` or `'any'` (default: `'file'`)
+
+: See also: {ref}`Channel.fromPath <channel-path>`.
+
+`files( filePattern, [options] )`
+: Convenience method for `file()` that always returns a list.
+
+`groupKey( key, size )`
+: Create a grouping key to use with the {ref}`operator-grouptuple` operator.
+
+`multiMapCriteria( closure )`
+: Create a multi-map criteria to use with the {ref}`operator-multiMap` operator.
+
+`sendMail( params )`
+: Send an email. See {ref}`mail-page`.
+
+`tuple( collection )`
+: Create a tuple object from the given collection.
+
+`tuple( ... args )`
+: Create a tuple object from the given arguments.
+
+`workflow.onComplete( closure )`
+: Define an action to take when the workflow completes (whether successful or not). Refer to the `workflow` implicit variable to see which additional properties are available in the completion handler.
+
+`workflow.onError( closure )`
+: Define an action to take if the workflow is terminated due to a runtime error or task failure. Refer to the `workflow` implicit variable to see which additional properties are available in the error handler.
+
+(stdlib-default-imports)=
+
+## Default imports
+
+The following classes are imported by default in Nextflow scripts:
+
+- `java.io.*`
+- `java.lang.*`
+- `java.math.BigDecimal`
+- `java.math.BigInteger`
+- `java.net.*`
+- `java.nio.file.Path`
+- `java.util.*`
+- `groovy.lang.*`
+- `groovy.util.*`
+
+## Channel
+
+The `Channel` class provides the channel factory methods. See {ref}`channel-factory` for more information.
+
+(stdlib-types-duration)=
+
+## Duration
+
+A `Duration` represents some duration of time.
+
+You can create a duration by adding a time unit suffix to an integer, e.g. `1.h`. The following suffixes are available:
+
+| Unit                            | Description  |
+| ------------------------------- | ------------ |
+| `ms`, `milli`, `millis`         | Milliseconds |
+| `s`, `sec`, `second`, `seconds` | Seconds      |
+| `m`, `min`, `minute`, `minutes` | Minutes      |
+| `h`, `hour`, `hours`            | Hours        |
+| `d`, `day`, `days`              | Days         |
+
+You can also create a duration with `Duration.of()`:
+
+```nextflow
+// integer value (milliseconds)
+oneSecond = Duration.of(1000)
+
+// simple string value
+oneHour = Duration.of('1h')
+
+// complex string value
+complexDuration = Duration.of('1day 6hours 3minutes 30seconds')
+```
+
+Durations can be compared like numbers, and they support basic arithmetic operations:
+
+```nextflow
+a = 1.h
+b = 2.h
+
+assert a < b
+assert a + a == b
+assert b - a == a
+assert a * 2 == b
+assert b / 2 == a
+```
+
+The following methods are available for a `Duration` object:
+
+`getDays()`, `toDays()`
+: Get the duration value in days (rounded down).
+
+`getHours()`, `toHours()`
+: Get the duration value in hours (rounded down).
+
+`getMillis()`, `toMillis()`
+: Get the duration value in milliseconds.
+
+`getMinutes()`, `toMinutes()`
+: Get the duration value in minutes (rounded down).
+
+`getSeconds()`, `toSeconds()`
+: Get the duration value in seconds (rounded down).
+
+(stdlib-types-memoryunit)=
+
+## MemoryUnit
+
+A `MemoryUnit` represents a quantity of bytes.
+
+You can create a memory unit by adding a unit suffix to an integer, e.g. `1.GB`. The following suffixes are available:
+
+| Unit | Description |
+| ---- | ----------- |
+| `B`  | Bytes       |
+| `KB` | Kilobytes   |
+| `MB` | Megabytes   |
+| `GB` | Gigabytes   |
+| `TB` | Terabytes   |
+| `PB` | Petabytes   |
+| `EB` | Exabytes    |
+| `ZB` | Zettabytes  |
+
+:::{note}
+Technically speaking, a kilobyte is equal to 1000 bytes, whereas 1024 bytes is called a "kibibyte" and abbreviated as "KiB", and so on for the other units. In practice, however, kilobyte is commonly understood to mean 1024 bytes, and Nextflow follows this convention in its implementation as well as this documentation.
+:::
+
+You can also create a memory unit with `MemoryUnit.of()`:
+
+```nextflow
+// integer value (bytes)
+oneKilobyte = MemoryUnit.of(1024)
+
+// string value
+oneGigabyte = MemoryUnit.of('1 GB')
+```
+
+Memory units can be compared like numbers, and they support basic arithmetic operations:
+
+```nextflow
+a = 1.GB
+b = 2.GB
+
+assert a < b
+assert a + a == b
+assert b - a == a
+assert a * 2 == b
+assert b / 2 == a
+```
+
+The following methods are available for a `MemoryUnit` object:
+
+`getBytes()`, `toBytes()`
+: Get the memory value in bytes (B).
+
+`getGiga()`, `toGiga()`
+: Get the memory value in gigabytes (rounded down), where 1 GB = 1024 MB.
+
+`getKilo()`, `toKilo()`
+: Get the memory value in kilobytes (rounded down), where 1 KB = 1024 B.
+
+`getMega()`, `toMega()`
+: Get the memory value in megabytes (rounded down), where 1 MB = 1024 KB.
+
+`toUnit( unit )`
+: Get the memory value in terms of a given unit (rounded down). The unit can be one of: `'B'`, `'KB'`, `'MB'`, `'GB'`, `'TB'`, `'PB'`, `'EB'`, `'ZB'`.
+
+(stdlib-types-path)=
+
+## Path
+
+The `file()` method returns a [Path](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/file/Path.html), so any method defined for Path can also be used in a Nextflow script.
+
+### Getting attributes
+
+The following methods are useful for getting attributes of a file:
+
+`exists()`
+: Returns `true` if the file exists.
+
+`getBaseName()`
+: Gets the file name without its extension, e.g. `/some/path/file.tar.gz` -> `file.tar`.
+
+`getExtension()`
+: Gets the file extension, e.g. `/some/path/file.txt` -> `txt`.
+
+`getName()`
+: Gets the file name, e.g. `/some/path/file.txt` -> `file.txt`.
+
+`getSimpleName()`
+: Gets the file name without any extension, e.g. `/some/path/file.tar.gz` -> `file`.
+
+`getParent()`
+: Gets the file parent path, e.g. `/some/path/file.txt` -> `/some/path`.
+
+`getScheme()`
+: Gets the file URI scheme, e.g. `s3://some-bucket/foo.txt` -> `s3`.
+
+`isDirectory()`
+: Returns `true` if the file is a directory.
+
+`isEmpty()`
+: Returns `true` if the file is empty or does not exist.
+
+`isFile()`
+: Returns `true` if it is a regular file (i.e. not a directory).
+
+`isHidden()`
+: Returns `true` if the file is hidden.
+
+`isLink()`
+: Returns `true` if the file is a symbolic link.
+
+`lastModified()`
+: Returns the file last modified timestamp in Unix time (i.e. milliseconds since January 1, 1970).
+
+`size()`
+: Gets the file size in bytes.
+
+`toUriString()`
+: Gets the file path along with the protocol scheme:
+  ```nextflow
+  def ref = file('s3://some-bucket/foo.txt')
+
+  assert ref.toString() == '/some-bucket/foo.txt'
+  assert "$ref" == '/some-bucket/foo.txt'
+  assert ref.toUriString() == 's3://some-bucket/foo.txt'
+  ```
+
+### Reading
+
+The following methods are available for reading files:
+
+`eachByte( closure )`
+: Iterates over the file byte by byte, applying the specified {ref}`closure <script-closure>`.
+
+`eachLine( closure )`
+: Iterates over the file line by line, applying the specified {ref}`closure <script-closure>`.
+
+`getBytes()`
+: Returns the file content as a byte array.
+
+`getText()`
+: Returns the file content as a string value.
+
+`newInputStream()`
+: Returns an [InputStream](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/InputStream.html) object to read a binary file.
+
+`newReader()`
+: Returns a [Reader](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/Reader.html) object to read a text file.
+
+`readLines()`
+: Reads the file line by line and returns the content as a list of strings.
+
+`withInputStream( closure )`
+: Opens a file for reading and lets you access it with an [InputStream](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/InputStream.html) object.
+
+`withReader( closure )`
+: Opens a file for reading and lets you access it with a [Reader](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/Reader.html) object.
+
+### Writing
+
+The following methods are available for writing to files:
+
+`append( text )`
+: Appends a string value to a file without replacing existing content.
+
+`newOutputStream()`
+: Creates an [OutputStream](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/OutputStream.html) object that allows you to write binary data to a file.
+
+`newPrintWriter()`
+: Creates a [PrintWriter](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/PrintWriter.html) object that allows you to write formatted text to a file.
+
+`newWriter()`
+: Creates a [Writer](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/Writer.html) object that allows you to save text data to a file.
+
+`setBytes( bytes )`
+: Writes a byte array to a file. Equivalent to setting the `bytes` property.
+
+`setText( text )`
+: Writes a string value to a file. Equivalent to setting the `text` property.
+
+`withOutputStream( closure )`
+: Applies the specified closure to an [OutputStream](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/OutputStream.html) object, closing it when finished.
+
+`withPrintWriter( closure )`
+: Applies the specified closure to a [PrintWriter](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/PrintWriter.html) object, closing it when finished.
+
+`withWriter( closure )`
+: Applies the specified closure to a [Writer](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/Writer.html) object, closing it when finished.
+
+`write( text )`
+: Writes a string to a file, replacing any existing content.
+
+### Filesystem operations
+
+The following methods are available for manipulating files and directories in a filesystem:
+
+`copyTo( target )`
+: Copies a source file or directory to a target file or directory.
+
+: *When copying a file to another file:* if the target file already exists, it will be replaced.
+
+  ```nextflow
+  file('/some/path/my_file.txt').copyTo('/another/path/new_file.txt')
+  ```
+
+: *When copying a file to a directory:* the file will be copied into the directory, replacing any file with the same name.
+
+  ```nextflow
+  file('/some/path/my_file.txt').copyTo('/another/path')
+  ```
+
+: *When copying a directory to another directory:* if the target directory already exists, the source directory will be copied into the target directory, replacing any sub-directory with the same name. If the target path does not exist, it will be created automatically.
+
+  ```nextflow
+  file('/any/dir_a').moveTo('/any/dir_b')
+  ```
+
+  The result of the above example depends on the existence of the target directory. If the target directory exists, the source is moved into the target directory, resulting in the path `/any/dir_b/dir_a`. If the target directory does not exist, the source is just renamed to the target name, resulting in the path `/any/dir_b`.
+
+: :::{note}
+  The `copyTo()` method follows the semantics of the Linux command `cp -r <source> <target>`, with the following caveat: while Linux tools often treat paths ending with a slash (e.g. `/some/path/name/`) as directories, and those not (e.g. `/some/path/name`) as regular files, Nextflow (due to its use of the Java files API) views both of these paths as the same file system object. If the path exists, it is handled according to its actual type (i.e. as a regular file or as a directory). If the path does not exist, it is treated as a regular file, with any missing parent directories created automatically.
+  :::
+
+`delete()`
+: Deletes the file or directory at the given path, returning `true` if the operation succeeds, and `false` otherwise:
+
+  ```nextflow
+  myFile = file('some/file.txt')
+  result = myFile.delete()
+  println result ? "OK" : "Cannot delete: $myFile"
+  ```
+
+  If a directory is not empty, it will not be deleted and `delete()` will return `false`.
+
+`deleteDir()`
+: Deletes a directory and all of its contents.
+
+  ```nextflow
+  file('any/path').deleteDir()
+  ```
+
+`getPermissions()`
+: Returns a file's permissions using the [symbolic notation](http://en.wikipedia.org/wiki/File_system_permissions#Symbolic_notation), e.g. `'rw-rw-r--'`.
+
+`list()`
+: Returns the first-level elements (files and directories) of a directory as a list of strings.
+
+`listFiles()`
+: Returns the first-level elements (files and directories) of a directory as a list of Paths.
+
+`mkdir()`
+: Creates a directory at the given path, returning `true` if the directory is created successfully, and `false` otherwise:
+
+  ```nextflow
+  myDir = file('any/path')
+  result = myDir.mkdir()
+  println result ? "OK" : "Cannot create directory: $myDir"
+  ```
+
+  If the parent directories do not exist, the directory will not be created and `mkdir()` will return `false`.
+
+`mkdirs()`
+: Creates a directory at the given path, including any nonexistent parent directories:
+
+  ```nextflow
+  file('any/path').mkdirs()
+  ```
+
+`mklink( linkName, [options] )`
+: Creates a *filesystem link* to a given path:
+
+  ```nextflow
+  myFile = file('/some/path/file.txt')
+  myFile.mklink('/user/name/link-to-file.txt')
+  ```
+
+  Available options:
+
+  `hard`
+  : When `true`, creates a *hard* link, otherwise creates a *soft* (aka *symbolic*) link (default: `false`).
+
+  `overwrite`
+  : When `true`, overwrites any existing file with the same name, otherwise throws a [FileAlreadyExistsException](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/file/FileAlreadyExistsException.html) (default: `false`).
+
+`moveTo( target )`
+: Moves a source file or directory to a target file or directory. Follows the same semantics as `copyTo()`.
+
+`renameTo( target )`
+: Rename a file or directory:
+
+  ```nextflow
+  file('my_file.txt').renameTo('new_file_name.txt')
+  ```
+
+`setPermissions( permissions )`
+: Sets a file's permissions using the [symbolic notation](http://en.wikipedia.org/wiki/File_system_permissions#Symbolic_notation):
+
+  ```nextflow
+  myFile.setPermissions('rwxr-xr-x')
+  ```
+
+`setPermissions( owner, group, other )`
+: Sets a file's permissions using the [numeric notation](http://en.wikipedia.org/wiki/File_system_permissions#Numeric_notation), i.e. as three digits representing the **owner**, **group**, and **other** permissions:
+
+  ```nextflow
+  myFile.setPermissions(7,5,5)
+  ```
+
+The following methods are available for listing and traversing directories:
+
+`eachDir( closure )`
+: Iterates through first-level directories only.
+
+`eachDirMatch( nameFilter, closure )`
+: Iterates through directories whose names match the given filter.
+
+`eachDirRecurse( closure )`
+: Iterates through directories depth-first (regular files are ignored).
+
+`eachFile( closure )`
+: Iterates through first-level files and directories.
+
+`eachFileMatch( nameFilter, closure )`
+: Iterates through files and directories whose names match the given filter.
+
+`eachFileRecurse( closure )`
+: Iterates through files and directories depth-first.
+
+Refer to the [Groovy documentation](http://docs.groovy-lang.org/latest/html/groovy-jdk/java/io/File.html) for more details.
+
+### Splitting files
+
+The following methods are available for splitting and counting the records in files:
+
+`countFasta()`
+: Counts the number of records in a [FASTA](https://en.wikipedia.org/wiki/FASTA_format) file. See the {ref}`operator-splitfasta` operator for available options.
+
+`countFastq()`
+: Counts the number of records in a [FASTQ](https://en.wikipedia.org/wiki/FASTQ_format) file. See the {ref}`operator-splitfastq` operator for available options.
+
+`countJson()`
+: Counts the number of records in a JSON file. See the {ref}`operator-splitjson` operator for available options.
+
+`countLines()`
+: Counts the number of lines in a text file. See the {ref}`operator-splittext` operator for available options.
+
+`splitCsv()`
+: Splits a CSV file into a list of records. See the {ref}`operator-splitcsv` operator for available options.
+
+`splitFasta()`
+: Splits a [FASTA](https://en.wikipedia.org/wiki/FASTA_format) file into a list of records. See the {ref}`operator-splitfasta` operator for available options.
+
+`splitFastq()`
+: Splits a [FASTQ](https://en.wikipedia.org/wiki/FASTQ_format) file into a list of records. See the {ref}`operator-splitfastq` operator for available options.
+
+`splitJson()`
+: Splits a JSON file into a list of records. See the {ref}`operator-splitjson` operator for available options.
+
+`splitText()`
+: Splits a text file into a list of lines. See the {ref}`operator-splittext` operator for available options.
diff --git a/docs/reference/syntax.md b/docs/reference/syntax.md
new file mode 100644
index 0000000000..06d7824527
--- /dev/null
+++ b/docs/reference/syntax.md
@@ -0,0 +1,942 @@
+(syntax-page)=
+
+# Syntax
+
+This page provides a comprehensive description of the Nextflow language.
+
+## Comments
+
+A line comment starts with `//` and includes the rest of the line.
+
+```nextflow
+println 'Hello world!' // line comment
+```
+
+A block comment starts with `/*` and includes all subsequent characters up to the first `*/`.
+
+```nextflow
+/*
+ * block comment
+ */
+println 'Hello again!'
+```
+
+## Top-level declarations
+
+A Nextflow script may contain the following top-level declarations:
+
+- Shebang
+- Feature flags
+- Includes
+- Parameter definitions
+- Workflow definitions
+- Process definitions
+- Function definitions
+- Enum types
+- Output block
+
+Script declarations are in turn composed of statements and expressions.
+
+If there are no top-level declarations, a script may contain one or more [statements](#statements), in which case the entire script is treated as an entry workflow. For example:
+
+```nextflow
+println 'Hello world!'
+```
+
+Is equivalent to:
+
+```nextflow
+workflow {
+    println 'Hello world!'
+}
+```
+
+:::{warning}
+Statements and top-level declarations can not be mixed at the same level. If your script has top-level declarations, all statements must be contained within top-level declarations such as the entry workflow.
+:::
+
+### Shebang
+
+The first line of a script can be a [shebang](https://en.wikipedia.org/wiki/Shebang_(Unix)):
+
+```sh
+#!/usr/bin/env nextflow
+```
+
+### Feature flag
+
+A feature flag declaration is an assignment. The target should be a valid {ref}`feature flag <config-feature-flags>` and the source should be a literal (i.e. number, string, boolean):
+
+```nextflow
+nextflow.preview.topic = true
+```
+
+### Include
+
+An include declaration consists of an *include source* and one or more *include clauses*:
+
+```nextflow
+include { foo as bar } from './some/module'
+```
+
+The include source should be a string literal and should refer to either a local path (e.g. `./module.nf`) or a plugin (e.g. `plugin/nf-hello`). Each include clause should specify a name, and may also specify an *alias*. In the above example, `foo` is included under the alias `bar`.
+
+Include clauses can be separated by semi-colons or newlines:
+
+```nextflow
+// semi-colons
+include { foo ; bar as baz } from './some/module'
+
+// newlines
+include {
+    foo
+    bar as baz
+} from './some/module'
+```
+
+Include clauses can also be specified as separate includes:
+
+```nextflow
+include { foo } from './some/module'
+include { bar as baz } from './some/module'
+```
+
+The following definitions can be included:
+
+- Functions
+- Processes
+- Named workflows
+
+### Parameter
+
+A parameter declaration is an assignment. The target should be a pipeline parameter and the source should be an expression:
+
+```nextflow
+params.message = 'Hello world!'
+```
+
+Parameters supplied via command line options, params files, and config files take precedence over parameter definitions in a script.
+
+(syntax-workflow)=
+
+### Workflow
+
+A workflow can be a *named workflow* or an *entry workflow*.
+
+A *named workflow* consists of a name and a body, and may consist of a *take*, *main*, *emit*, and *publish* section:
+
+```nextflow
+workflow greet {
+    take:
+    greetings
+
+    main:
+    messages = greetings.map { v -> "$v world!" }
+
+    emit:
+    messages
+}
+```
+
+- The take, emit, and publish sections are optional. The `main:` section label can be omitted if they are not specified.
+
+- The take section consists of one or more parameters.
+
+- The main section consists of one or more [statements](#statements).
+
+- The emit section consists of one or more *emit statements*. An emit statement can be a [variable name](#variable), an [assignment](#assignment), or an [expression statement](#expression-statement). If an emit statement is an expression statement, it must be the only emit.
+
+- The publish section can be specified but is intended to be used in the entry workflow (see below).
+
+
+An *entry workflow* has no name and may consist of a *main* and *publish* section:
+
+```nextflow
+workflow {
+    main:
+    greetings = Channel.of('Bonjour', 'Ciao', 'Hello', 'Hola')
+    messages = greetings.map { v -> "$v world!" }
+    greetings.view { it -> '$it world!' }
+
+    publish:
+    messages >> 'messages'
+}
+```
+
+- Only one entry workflow may be defined in a script.
+
+- The `main:` section label can be omitted if the publish section is not specified.
+
+- The publish section consists of one or more *publish statements*. A publish statement is a [right-shift expression](#binary-expressions), where the left-hand side is an expression that refers to a value in the workflow body, and the right-hand side is an expression that returns a string.
+
+In order for a script to be executable, it must either define an entry workflow or use the implicit workflow syntax described [above](#top-level-declarations).
+
+Entry workflow definitions are ignored when a script is included as a module. This way, the same script can be included as a module or executed as a pipeline.
+
+(syntax-process)=
+
+### Process
+
+A process consists of a name and a body. The process body consists of one or more [statements](#statements). A minimal process definition must return a string:
+
+```nextflow
+process sayHello {
+    """
+    echo 'Hello world!'
+    """
+}
+```
+
+A process may define additional sections for *directives*, *inputs*, *outputs*, *script*, *exec*, and *stub*:
+
+```nextflow
+process greet {
+    // directives
+    errorStrategy 'retry'
+    tag { "${greeting}/${name}" }
+
+    input: 
+    val greeting
+    val name
+
+    output:
+    stdout
+
+    script: // or exec:
+    """
+    echo '${greeting}, ${name}!'
+    """
+
+    stub:
+    """
+    # do nothing
+    """
+}
+```
+
+- A process must define a script or exec section (see below). All other sections are optional. Directives do not have an explicit section label, but must be defined first.
+
+- The `script:` section label can be omitted only when there are no other sections in the body.
+
+- Sections must be defined in the order shown above, with the exception of the output section, which can also be specified after the script and stub.
+
+Each section may contain one or more statements. For directives, inputs, and outputs, these statements must be [function calls](#function-call). See {ref}`process-reference` for the set of available input qualifiers, output qualifiers, and directives.
+
+The script section can be substituted with an exec section:
+
+```nextflow
+process greetExec {
+    input: 
+    val greeting
+    val name
+
+    exec:
+    message = "${greeting}, ${name}!"
+
+    output:
+    val message
+}
+```
+
+The script and stub sections must return a string in the same manner as a [function](#function).
+
+See {ref}`process-page` for more information on the semantics of each process section.
+
+(syntax-function)=
+
+### Function
+
+A function consists of a name, parameter list, and a body:
+
+```nextflow
+def greet(greeting, name) {
+    println "${greeting}, ${name}!"
+}
+```
+
+The function body consists of one or more [statements](#statements). The last statement is implicitly treated as a return statement if it is an [expression statement](#expression-statement) that returns a value.
+
+The [return statement](#return) can be used to explicitly return from a function:
+
+```nextflow
+// return with no value
+def greet(greeting, name) {
+    if( !greeting || !name )
+        return
+    println "${greeting}, ${name}!"
+}
+
+// return a value
+def fib(x) {
+    if( x <= 1 )
+        return x
+    fib(x - 1) + fib(x - 2)
+}
+```
+
+### Enum type
+
+An enum type declaration consists of a name and a body. The body consists of a comma-separated list of identifiers:
+
+```nextflow
+enum Day {
+    MONDAY,
+    TUESDAY,
+    WEDNESDAY,
+    THURSDAY,
+    FRIDAY,
+    SATURDAY,
+    SUNDAY
+}
+```
+
+Enum values in the above example can be accessed as `Day.MONDAY`, `Day.TUESDAY`, and so on.
+
+:::{note}
+Enum types cannot be included across modules at this time.
+:::
+
+### Output block
+
+The output block consists of one or more *target blocks*. A target block consists of a *target name* and one or more *target directives* for configuring the corresponding publish target:
+
+```nextflow
+output {
+    'fastq' {
+        path 'samples'
+        index {
+            path 'index.csv'
+        }
+    }
+}
+```
+
+Only one output block may be defined in a script. See {ref}`workflow-output-def` for the set of available target directives.
+
+## Statements
+
+Statements can be separated by either a newline or a semi-colon:
+
+```nextflow
+// newline
+println 'Hello!'
+println 'Hello again!'
+
+// semi-colon
+println 'Hello!' ; println 'Hello again!'
+```
+
+### Variable declaration
+
+Variables can be declared with the `def` keyword:
+
+```nextflow
+def x = 42
+```
+
+Multiple variables can be declared in a single statement if the initializer is a [list literal](#list) with the same number of elements and declared variables:
+
+```nextflow
+def (x, y) = [ 1, 2 ]
+```
+
+Each variable has a *scope*, which is the region of code in which the variable can be used.
+
+Variables declared in a function, as well as the parameters of that function, exist for the duration of that function call. The same applies to closures.
+
+Workflow inputs exist for the entire workflow body. Variables declared in the main section exist for the main, emit, and publish sections. Named outputs are not considered variable declarations and therefore do not have any scope.
+
+Process input variables exist for the entire process body. Variables declared in the process script, exec, and stub sections exist only in their respective section, with one exception -- variables declared without the `def` keyword also exist in the output section.
+
+Variables declared in an if or else branch exist only within that branch:
+
+```nextflow
+if( true )
+    def x = 'foo'
+println x           // error: `x` is undefined
+
+// solution: declare `x` outside of if branch
+def x
+if( true )
+    x = 'foo'
+println x
+```
+
+A variable cannot be declared with the same name as another variable in the same scope or an enclosing scope:
+
+```nextflow
+def clash(x) {
+    def x           // error: `x` is already declared
+    if( true )
+        def x       // error: `x` is already declared
+}
+```
+
+### Assignment
+
+An assignment statement consists of a *target* expression and a *source* expression separated by an equals sign:
+
+```nextflow
+v = 42
+list[0] = 'first'
+map.key = 'value'
+```
+
+The target expression must be a [variable](#variable), [index](#binary-expressions), or [property](#binary-expressions) expression. The source expression can be any expression.
+
+Multiple variables can be assigned in a single statement as long as the source expression is a [list literal](#list) with the same number of elements and assigned variables:
+
+```nextflow
+(x, y) = [ 1, 2 ]
+```
+
+### Expression statement
+
+Any [expression](#expressions) can be a statement.
+
+In general, the only expressions that can have any effect as expression statements are function calls that have side effects (e.g. `println`) or an implicit return statement in a [function](#function) or [closure](#closure).
+
+### assert
+
+An assert statement consists of the `assert` keyword followed by a boolean expression, with an optional error message separated by a colon:
+
+```nextflow
+assert 2 + 2 == 4 : 'The math broke!'
+```
+
+If the condition is false, an error will be raised with the given error message.
+
+### if/else
+
+An if/else statement consists of an *if branch* and an optional *else branch*. Each branch consists of a boolean expression in parentheses, followed by either a single statement or a *block statement* (one or more statements in curly braces). For example:
+
+```nextflow
+def x = Math.random()
+if( x < 0.5 ) {
+    println 'You lost.'
+}
+else {
+    println 'You won!'
+}
+```
+
+If the condition is true, the if branch will be executed, otherwise the else branch will be executed.
+
+If/else statements can be chained any number of times by making the else branch another if/else statement:
+
+```nextflow
+def grade = 89
+if( grade >= 90 )
+    println 'You get an A!'
+else if( grade >= 80 )
+    println 'You get a B!'
+else if( grade >= 70 )
+    println 'You get a C!'
+else if( grade >= 60 )
+    println 'You get a D!'
+else
+    println 'You failed.'
+```
+
+A more verbose way to write the same code is:
+
+```nextflow
+def grade = 89
+if( grade >= 90 ) {
+    println 'You get an A!'
+}
+else {
+    if( grade >= 80 ) {
+        println 'You get a B!'
+    }
+    else {
+        if( grade >= 70 ) {
+            println 'You get a C!'
+        }
+        else {
+            if( grade >= 60 ) {
+                println 'You get a D!'
+            }
+            else {
+                println 'You failed.'
+            }
+        }
+    }
+}
+```
+
+### return
+
+A return statement consists of the `return` keyword with an optional expression:
+
+```nextflow
+def add(a, b) {
+    return a + b
+}
+
+def sayHello(name) {
+    if( !name )
+        return
+    println "Hello, ${name}!"
+}
+```
+
+Return statements can only be used in functions and closures. In the case of a nested closure, the return statement will return from the nearest enclosing closure.
+
+If a function or closure has multiple return statements (including implicit returns), all of the return statements should either return a value or return nothing. If a function or closure does return a value, it should do so for every conditional branch.
+
+```nextflow
+def isEven1(n) {
+    if( n % 2 == 1 )
+        return          // error: return value is required here
+    return true
+}
+
+def isEven2(n) {
+    if( n % 2 == 0 )
+        return true
+                        // error: return value is required here
+}
+```
+
+:::{note}
+If the last statement is not a return or expression statement (implicit return), it is equivalent to appending an empty return.
+:::
+
+### throw
+
+A throw statement consists of the `throw` keyword followed by an expression that returns an error type:
+
+```nextflow
+throw new Exception('something failed!')
+```
+
+:::{note}
+In general, the appropriate way to raise an error is to use the {ref}`error <stdlib-functions>` function:
+```nextflow
+error 'something failed!'
+```
+:::
+
+### try/catch
+
+A try/catch statement consists of a *try block* followed by any number of *catch clauses*:
+
+```nextflow
+def text = null
+try {
+    text = file('foo.txt').text
+}
+catch( IOException e ) {
+    log.warn "Could not load foo.txt"
+}
+```
+
+The try block will be executed, and if an error is raised and matches the expected error type of a catch clause, the code in that catch clause will be executed. If no catch clause is matched, the error will be raised to the next enclosing try/catch statement, or to the Nextflow runtime.
+
+## Expressions
+
+An expression represents a value. A *literal* value is an expression whose value is known at compile-time, such as a number, string, or boolean. All other expressions must be evaluated at run-time.
+
+Every expression has a *type*, which may be resolved at compile-time or run-time.
+
+### Variable
+
+A variable expression is a reference to a variable or other named value:
+
+```nextflow
+def x = 42
+
+x
+// -> 42
+```
+
+### Number
+
+A number literal can be an integer or floating-point number, and can be positive or negative. Integers can specified in binary with `0b`, octal with `0`, or hexadecimal with `0x`. Floating-point numbers can use scientific notation with the `e` or `E` prefix. Underscores can be used as thousands separators to make long numbers more readable.
+
+```nextflow
+// integer
+42
+-1
+0b1001  // -> 9
+031     // -> 25
+0xabcd  // -> 43981
+
+// real
+3.14
+-0.1
+1.59e7  // -> 15_900_000
+1.59e-7 // -> 0.000000159
+```
+
+### Boolean
+
+A boolean literal can be `true` or `false`:
+
+```nextflow
+assert true != false
+assert !true == false
+assert true == !false
+```
+
+### Null
+
+The null literal is specified as `null`. It can be used to represent an "empty" value:
+
+```nextflow
+def x = null
+x = 42
+```
+
+:::{note}
+Using a null value in certain expressions (e.g. the object of a property expression or method call) will lead to a "null reference" error. It is best to avoid the use of `null` where possible.
+:::
+
+### String
+
+A string literal consists of arbitrary text enclosed by single or double quotes:
+
+```nextflow
+println "I said 'hello'"
+println 'I said "hello" again!'
+```
+
+A triple-quoted string can span multiple lines:
+
+```nextflow
+println '''
+    Hello,
+    How are you today?
+    '''
+
+println """
+    We don't have to escape quotes anymore!
+    Even "double" quotes!
+    """
+```
+
+A *slashy string* is enclosed by slashes instead of quotes:
+
+```nextflow
+/no escape!/
+```
+
+:::{note}
+A slashy string cannot be empty because it would become a line comment.
+:::
+
+### Dynamic string
+
+Double-quoted strings can be interpolated using the `${}` placeholder with an expression:
+
+```nextflow
+def names = ['Thing 1', 'Thing 2']
+println "Hello, ${names.join(' and ')}!"
+// -> Hello, Thing 1 and Thing 2!
+```
+
+If the expression is a name or simple property expression (one or more identifiers separated by dots), the curly braces can be omitted:
+
+```nextflow
+def name = [first: '<FIRST_NAME>', last: '<LAST_NAME>']
+println "Hello, ${name.first} ${name.last}!"
+// -> Hello, <FIRST_NAME> <LAST_NAME>!
+```
+
+Multi-line double-quoted strings can also be interpolated:
+
+```nextflow
+"""
+blastp \
+    -in $input \
+    -out $output \
+    -db $blast_db \
+    -html
+"""
+```
+
+Single-quoted strings are not interpolated:
+
+```nextflow
+println 'Hello, ${names.join(" and ")}!'
+// -> Hello, ${names.join(" and ")}!
+```
+
+### List
+
+A list literal consists of a comma-separated list of zero or more expressions, enclosed in square brackets:
+
+```nextflow
+[1, 2, 3]
+```
+
+### Map
+
+A map literal consists of a comma-separated list of one or more *map entries*, enclosed in square brackets. Each map entry consists of a *key expression* and *value expression* separated by a colon:
+
+```nextflow
+[foo: 1, bar: 2, baz: 3]
+```
+
+An empty map is specified with a single colon to distinguish it from an empty list:
+
+```nextflow
+[:]
+```
+
+Both the key and value can be any expression. Identifier keys are treated as string literals (i.e. the quotes can be omitted). A variable can be used as a key by enclosing it in parentheses:
+
+```nextflow
+def x = 'foo'
+[(x): 1]
+// -> ['foo': 1]
+```
+
+### Closure
+
+A closure, also known as an anonymous function, consists of a parameter list followed by zero or more statements, enclosed in curly braces:
+
+```nextflow
+{ a, b -> a + b }
+```
+
+The above closure takes two arguments and returns their sum.
+
+The closure body is identical to that of a [function](#function). Statements should be separated by newlines or semi-colons, and the last statement is implicitly treated as a [return statement](#return):
+
+```nextflow
+{ v ->
+    println 'Hello!'
+    println "We're in a closure!"
+    println 'Goodbye...'
+    v * v
+}
+```
+
+Closures can access variables outside of their scope:
+
+```nextflow
+def factor = 2
+println [1, 2, 3].collect { v -> factor * v }
+// -> [2, 4, 6]
+```
+
+Closures can declare local variables that exist only for the lifetime of each closure invocation:
+
+```nextflow
+def result = 0
+[1, 2, 3].each { v ->
+    def squared = v * v
+    result += squared
+}
+
+println result
+// -> 14
+```
+
+See {ref}`standard library <stdlib-page>` and {ref}`operator <operator-page>` for more examples of how closures are used in practice.
+
+### Index expression
+
+An index expression consists of a *left expression* and a *right expression*, with the right expression enclosed in square brackets:
+
+```nextflow
+myList[0]
+```
+
+### Property expression
+
+A property expression consists of an *object expression* and a *property*, separated by a *dot*, *spread dot*, or *safe dot*:
+
+```nextflow
+myFile.text       // dot
+myFiles*.text     // spread dot:  myFiles.collect { myFile -> myFile.text }
+myFile?.text      // safe dot:    myFile != null ? myFile.text : null
+```
+
+The property must be an identifier or string literal.
+
+### Function call
+
+A function call consists of a name and argument list:
+
+```nextflow
+printf('Hello %s!\n', 'World')
+```
+
+A *method call* consists of an *object expression* and a function call separated by a *dot*, *spread dot*, or *safe dot*:
+
+```nextflow
+myFile.getText()    // dot
+myFiles*.getText()  // spread dot:  myFiles.collect { myFile -> myFile.getText() }
+myFile?.getText()   // safe dot:    myFile != null ? myFile.getText() : null
+```
+
+The argument list may contain any number of *positional arguments* and *named arguments*:
+
+```nextflow
+file('hello.txt', checkIfExists: true)
+```
+
+The named arguments are collected into a map and provided as the first positional argument to the function. The above function call can be rewritten as:
+
+```nextflow
+file([checkIfExists: true], 'hello.txt')
+```
+
+The argument name must be an identifier or string literal.
+
+The parentheses can be omitted when the function call is also an [expression statement](#expression-statement) and there is at least one argument:
+
+```nextflow
+// positional args
+printf 'Hello %s!\n', 'World'
+
+// positional and named args
+file 'hello.txt', checkIfExists: true
+```
+
+If the last argument is a closure, it can be specified outside of the parentheses:
+
+```nextflow
+// closure arg with additional args
+[1, 2, 3].inject('result:') { acc, v -> acc + ' ' + v }
+
+// single closure arg
+[1, 2, 3].each() { v -> println v }
+
+// single closure arg without parentheses
+[1, 2, 3].each { v -> println v }
+```
+
+### Constructor call
+
+A constructor call consists of the `new` keyword followed by a *type name* and an argument list enclosed in parentheses:
+
+```nextflow
+new java.util.Date()
+```
+
+If the type is implicitly available in the script, the *fully-qualified type name* can be elided to the *simple type name*:
+
+```nextflow
+new Date()
+```
+
+See {ref}`stdlib-default-imports` for the set of types which are implicitly available in Nextflow scripts.
+
+### Unary expressions
+
+A unary expression consists of a *unary operator* followed by an expression:
+
+```nextflow
+!(2 + 2 == 4)
+```
+
+The following unary operators are available:
+
+- `~`: bitwise NOT
+- `!`: logical NOT
+- `+`: unary plus
+- `-`: unary minus
+
+### Binary expressions
+
+A binary expression consists of a *left expression* and a *right expression* separated by a *binary operator*:
+
+```nextflow
+2 + 2
+```
+
+The following binary operators are available:
+
+- `**`: power (i.e. exponentiation)
+- `*`: multiplication
+- `/`: division
+- `%`: remainder (i.e. modulo)
+- `+`: addition
+- `-`: subtraction
+- `<<`: left shift
+- `>>`: right shift
+- `>>>`: unsigned right shift
+- `..`: inclusive range
+- `..<`: right-exclusive range
+- `as`: type cast
+- `instanceof`: type relation
+- `!instanceof`: negated type relation
+- `<`: less than
+- `>`: greater than
+- `<=`: less than or equals
+- `>=`: greater than or equals
+- `in`: membership
+- `!in`: negated membership
+- `==`: equals
+- `!=`: negated equals
+- `<=>`: spaceship (i.e. three-way comparison)
+- `=~`: regex find
+- `==~`: regex match
+- `&`: bitwise AND
+- `^`: bitwise XOR (exclusive or)
+- `|`: bitwise OR
+- `&&`: logical AND
+- `||`: logical OR
+- `?:` elvis (i.e. short ternary)
+
+### Ternary expression
+
+A ternary expression consists of a *test expression*, a *true expression*, and a *false expression*, separated by a question mark and a colon:
+
+```nextflow
+println x % 2 == 0 ? 'x is even!' : 'x is odd!'
+```
+
+If the test expression is true, the true expression is evaluated, otherwise the false expression is evaluated.
+
+### Parentheses
+
+Any expression can be enclosed in parentheses:
+
+```nextflow
+1 + 2 * 3
+// -> 1 + 6 -> 7
+
+(1 + 2) * 3
+// -> 3 * 3 -> 9
+```
+
+### Precedence
+
+Compound expressions are evaluated in the following order:
+
+- parentheses
+- property expressions
+- function calls
+- index expressions
+- `~`,  `!`
+- `**`
+- `+`, `-` (unary)
+- `*`, `/`, `%`
+- `+`, `-` (binary)
+- `<<`, `>>>`, `>>`, `..`, `..<`
+- `as`
+- `instanceof`, `!instanceof`
+- `<`, `>`, `<=`, `>=`, `in`, `!in`
+- `==`, `!=`, `<=>`
+- `=~`, `==~`
+- `&`
+- `^`
+- `|`
+- `&&`
+- `||`
+- `?:` (ternary)
+- `?:` (elvis)
+
+## Deprecations
+
+The following legacy features were excluded from this page because they are deprecated:
+
+- The `addParams` and `params` clauses of include declarations. See {ref}`module-params` for more information.
+- The `when:` section of a process definition. See {ref}`process-when` for more information.
+- The `shell:` section of a process definition. See {ref}`process-shell` for more information.
+- The implicit `it` closure parameter. See {ref}`script-closure` for more information.
diff --git a/docs/tracing.md b/docs/reports.md
similarity index 95%
rename from docs/tracing.md
rename to docs/reports.md
index 6c0b6780cb..c208c123c9 100644
--- a/docs/tracing.md
+++ b/docs/reports.md
@@ -13,7 +13,7 @@ nextflow log <run name> [options]
 ```
 
 :::{note}
-Both the {ref}`execution report <execution-report>` and the {ref}`trace report <trace-report>` must be specified when the pipeline is first called. By contrast, the `log` option is useful after a pipeline has already run and is available for every executed pipeline.
+Both the [execution report](#execution-report) and the [trace file](#trace-file) must be specified when the pipeline is first called. By contrast, the `log` option is useful after a pipeline has already run and is available for every executed pipeline.
 :::
 
 By default, `log` prints the list of executed pipelines:
@@ -121,7 +121,7 @@ Plots are shown for CPU, memory, job duration and disk I/O. They have two (or th
 ```{image} _static/report-resource-cpu.png
 ```
 
-Learn more about how resource usage is computed in the {ref}`Metrics documentation <metrics-page>`.
+Learn more about how resource usage is computed in {ref}`this tutorial <metrics-page>`.
 
 (execution-report-tasks)=
 
@@ -133,7 +133,7 @@ The `Tasks` section lists all executed tasks, reporting for each of them the sta
 ```
 
 :::{note}
-Nextflow collects these metrics through a background process for each job in the target environment. Make sure the following tools are available in the environment where tasks are executed: `awk`, `date`, `grep`, `ps`, `sed`, `tail`, `tee`. Moreover, some of these metrics are not reported when running on Mac OS X. See the note about that in the [Trace report](#trace-report) below.
+Nextflow collects these metrics through a background process for each job in the target environment. Make sure the following tools are available in the environment where tasks are executed: `awk`, `date`, `grep`, `ps`, `sed`, `tail`, `tee`. Moreover, some of these metrics are not reported when running on Mac OS X. See the corresponding note in the [trace file](#trace-file) section.
 :::
 
 :::{warning}
@@ -144,7 +144,7 @@ Please read {ref}`Report scope <config-report>` section to learn more about the
 
 (trace-report)=
 
-## Trace report
+## Trace file
 
 Nextflow creates an execution tracing file that contains some useful information about each process executed in your pipeline script, including: submission time, start time, completion time, cpu and memory used.
 
@@ -180,6 +180,8 @@ It will create a file named `trace.txt` in the current directory. The content lo
 
 (trace-fields)=
 
+### Trace fields
+
 The following table shows the fields that can be included in the execution report:
 
 `task_id`
@@ -322,9 +324,9 @@ Please read {ref}`Trace scope <config-trace>` section to learn more about it.
 
 (timeline-report)=
 
-## Timeline report
+## Execution timeline
 
-Nextflow can render an HTML timeline for all processes executed in your pipeline. An example of the timeline report is shown below:
+Nextflow can render an HTML timeline for all processes executed in your pipeline. An example of the execution timeline is shown below:
 
 ```{image} _static/timeline-min.png
 ```
@@ -335,7 +337,7 @@ Each bar displays two numbers: the task duration time and the virtual memory siz
 
 As each process can spawn many tasks, colors are used to identify those tasks belonging to the same process.
 
-To enable the creation of the timeline report add the `-with-timeline` command line option when launching the pipeline execution. For example:
+To enable the creation of the execution timeline add the `-with-timeline` command line option when launching the pipeline execution. For example:
 
 ```bash
 nextflow run <pipeline> -with-timeline [file name]
@@ -343,9 +345,9 @@ nextflow run <pipeline> -with-timeline [file name]
 
 The report file name can be specified as an optional parameter following the timeline option.
 
-(dag-visualisation)=
+(workflow-diagram)=
 
-## DAG visualisation
+## Workflow diagram
 
 A Nextflow pipeline can be represented as a direct acyclic graph (DAG). The vertices in the graph represent the pipeline's processes and operators, while the edges represent the data dependencies (i.e. channels) between them.
 
diff --git a/docs/script.md b/docs/script.md
index 3b7ea19642..eec9320ffe 100644
--- a/docs/script.md
+++ b/docs/script.md
@@ -2,17 +2,9 @@
 
 # Scripts
 
-The Nextflow scripting language is an extension of the Groovy programming language. Groovy is a powerful programming language for the Java virtual machine. The Nextflow syntax has been specialized to ease the writing of computational pipelines in a declarative manner.
+Nextflow is a workflow language that runs on the Java virtual machine (JVM). Nextflow's syntax is very similar to [Groovy](https://groovy-lang.org/), a scripting language for the JVM. However, Nextflow is specialized for writing computational pipelines in a declarative manner. See {ref}`syntax-page` for a full description of the Nextflow language.
 
-Nextflow can execute any piece of Groovy code or use any library for the JVM platform.
-
-For a detailed description of the Groovy programming language, reference these links:
-
-- [Groovy User Guide](http://groovy-lang.org/documentation.html)
-- [Groovy Cheat sheet](http://www.cheat-sheets.org/saved-copy/rc015-groovy_online.pdf)
-- [Groovy in Action](http://www.manning.com/koenig2/)
-
-Below you can find a crash course in the most important language constructs used in the Nextflow scripting language.
+Nextflow scripts can also make full use of the Java and Groovy standard libraries. See {ref}`stdlib-page` for more information.
 
 :::{warning}
 Nextflow uses UTF-8 as the default character encoding for source files. Make sure to use UTF-8 encoding when editing Nextflow scripts with your preferred text editor.
@@ -22,93 +14,90 @@ Nextflow uses UTF-8 as the default character encoding for source files. Make sur
 Nextflow scripts have a maximum size of 64 KiB. To avoid this limit for large pipelines, consider moving pipeline components into separate files and including them as modules.
 :::
 
-## Groovy basics
+## Hello world
 
-### Hello world
+You can use the `println` function to print to the console:
 
-To print something is as easy as using one of the `print` or `println` methods.
-
-```groovy
-println "Hello, World!"
+```nextflow
+println 'Hello, World!'
 ```
 
-The only difference between the two is that the `println` method implicitly appends a newline character to the printed string.
 
-### Variables
+## Variables
 
-To define a variable, simply assign a value to it:
+Variables are declared using the `def` keyword:
 
-```groovy
-x = 1
-println x
+```nextflow
+def num = 1
+println num
 
-x = new java.util.Date()
-println x
+def date = new java.util.Date()
+println date
 
-x = -3.1499392
+def x = -3.1499392
 println x
 
-x = false
-println x
+def flag = false
+println flag
 
-x = "Hi"
-println x
+def str = "Hi"
+println str
 ```
 
-### Lists
+:::{warning}
+Variables can also be declared without `def` in some cases. However, this practice is discouraged outside of simple code snippets because it can lead to a {ref}`race condition <cache-global-var-race-condition>`.
+:::
+
+## Lists
 
-A List object can be defined by placing the list items in square brackets:
+Lists are defined using square brackets:
 
-```groovy
-myList = [1776, -1, 33, 99, 0, 928734928763]
+```nextflow
+def myList = [1776, -1, 33, 99, 0, 928734928763]
 ```
 
 You can access a given item in the list with square-bracket notation (indexes start at 0):
 
-```groovy
+```nextflow
 println myList[0]
 ```
 
 In order to get the length of the list use the `size` method:
 
-```groovy
+```nextflow
 println myList.size()
 ```
 
-Learn more about lists:
-
-- [Groovy Lists tutorial](http://groovy-lang.org/groovy-dev-kit.html#Collections-Lists)
-- [Groovy List API](http://docs.groovy-lang.org/latest/html/groovy-jdk/java/util/List.html)
-- [Java List API](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/util/List.html)
+Refer to the [Java](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/util/List.html) and [Groovy](http://docs.groovy-lang.org/latest/html/groovy-jdk/java/util/List.html) standard libraries for the set of available list operations.
 
-### Maps
+## Maps
 
 Maps are used to store *associative arrays* (also known as *dictionaries*). They are unordered collections of heterogeneous, named data:
 
-```groovy
-scores = ["Brett": 100, "Pete": "Did not finish", "Andrew": 86.87934]
+```nextflow
+def scores = ["Brett": 100, "Pete": "Did not finish", "Andrew": 86.87934]
 ```
 
 Note that each of the values stored in the map can be of a different type. `Brett` is an integer, `Pete` is a string, and `Andrew` is a floating-point number.
 
 We can access the values in a map in two main ways:
 
-```groovy
+```nextflow
 println scores["Pete"]
 println scores.Pete
 ```
 
 To add data to or modify a map, the syntax is similar to adding values to list:
 
-```groovy
+```nextflow
 scores["Pete"] = 3
 scores["Cedric"] = 120
 ```
 
 You can also use the `+` operator to add two maps together:
 
-```groovy
-new_scores = scores + ["Pete": 3, "Cedric": 120]
+```nextflow
+def new_scores = scores + ["Pete": 3, "Cedric": 120]
 ```
 
 When adding two maps, the first map is copied and then appended with the keys from the second map. Any conflicting keys are overwritten by the second map.
@@ -117,33 +106,14 @@ When adding two maps, the first map is copied and then appended with the keys fr
 Copying a map with the `+` operator is a safer way to modify maps in Nextflow, specifically when passing maps through channels. This way, a new instance of the map will be created, and any references to the original map won't be affected.
 :::
 
-Learn more about maps:
+See the [Java](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/util/Map.html) and [Groovy](http://docs.groovy-lang.org/latest/html/groovy-jdk/java/util/Map.html) standard libraries for the set of available map operations.
 
-- [Groovy Maps tutorial](http://groovy-lang.org/groovy-dev-kit.html#Collections-Maps)
-- [Groovy Map API](http://docs.groovy-lang.org/latest/html/groovy-jdk/java/util/Map.html)
-- [Java Map API](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/util/Map.html)
-
-(script-multiple-assignment)=
-
-### Multiple assignment
-
-An array or a list object can used to assign to multiple variables at once:
-
-```groovy
-(a, b, c) = [10, 20, 'foo']
-assert a == 10 && b == 20 && c == 'foo'
-```
-
-The three variables on the left of the assignment operator are initialized by the corresponding item in the list.
-
-Read more about [Multiple assignment](http://www.groovy-lang.org/semantics.html#_multiple_assignment) in the Groovy documentation.
-
-### Conditional Execution
+## Conditional execution
 
 One of the most important features of any programming language is the ability to execute different code under different conditions. The simplest way to do this is to use the `if` construct:
 
-```groovy
-x = Math.random()
+```nextflow
+def x = Math.random()
 if( x < 0.5 ) {
     println "You lost."
 }
@@ -152,19 +122,19 @@ else {
 }
 ```
 
-### Strings
+## Strings
 
 Strings can be defined by enclosing text in single or double quotes (`'` or `"` characters):
 
-```groovy
+```nextflow
 println "he said 'cheese' once"
 println 'he said "cheese!" again'
 ```
 
 Strings can be concatenated with `+`:
 
-```groovy
-a = "world"
+```nextflow
+def a = "world"
 print "hello " + a + "\n"
 ```
 
@@ -176,12 +146,12 @@ There is an important difference between single-quoted and double-quoted strings
 
 In practice, double-quoted strings can contain the value of an arbitrary variable by prefixing its name with the `$` character, or the value of any expression by using the `${expression}` syntax, similar to Bash/shell scripts:
 
-```groovy
-foxtype = 'quick'
-foxcolor = ['b', 'r', 'o', 'w', 'n']
+```nextflow
+def foxtype = 'quick'
+def foxcolor = ['b', 'r', 'o', 'w', 'n']
 println "The $foxtype ${foxcolor.join()} fox"
 
-x = 'Hello'
+def x = 'Hello'
 println '$x + $y'
 ```
 
@@ -196,8 +166,8 @@ $x + $y
 
 A block of text that span multiple lines can be defined by delimiting it with triple single or double quotes:
 
-```groovy
-text = """
+```nextflow
+def text = """
     hello there James
     how are you today?
     """
@@ -209,8 +179,8 @@ Like before, multi-line strings inside double quotes support variable interpolat
 
 As in Bash/shell scripts, terminating a line in a multi-line string with a `\` character prevents a newline character from separating that line from the one that follows:
 
-```groovy
-myLongCmdline = """
+```nextflow
+def myLongCmdline = """
     blastp \
     -in $input_query \
     -out $output_file \
@@ -218,13 +188,13 @@ myLongCmdline = """
     -html
     """
 
-result = myLongCmdline.execute().text
+def result = myLongCmdline.execute().text
 ```
 
 In the preceding example, `blastp` and its `-in`, `-out`, `-db` and `-html` switches and their arguments are effectively a single line.
 
 :::{warning}
-When using backslashes to continue a multi-line command, make sure to not put any spaces after the backslash, otherwise it will be interpreted by the Groovy lexer as an escaped space instead of a backslash, which will make your script incorrect. It will also print this warning:
+Do not put any spaces after the backslash when using backslashes to continue a multi-line command. Spaces after the backslash will be interpreted as an escaped space and will make your script incorrect. It will also print this warning:
 
 ```
 unknown recognition error type: groovyjarjarantlr4.v4.runtime.LexerNoViableAltException
@@ -233,7 +203,7 @@ unknown recognition error type: groovyjarjarantlr4.v4.runtime.LexerNoViableAltEx
 
 (script-regexp)=
 
-### Regular expressions
+## Regular expressions
 
 Regular expressions are the Swiss Army knife of text processing. They provide the programmer with the ability to match and extract patterns from strings.
 
@@ -241,21 +211,21 @@ Regular expressions are available via the `~/pattern/` syntax and the `=~` and `
 
 Use `=~` to check whether a given pattern occurs anywhere in a string:
 
-```groovy
+```nextflow
 assert 'foo' =~ /foo/       // return TRUE
 assert 'foobar' =~ /foo/    // return TRUE
 ```
 
 Use `==~` to check whether a string matches a given regular expression pattern exactly.
 
-```groovy
+```nextflow
 assert 'foo' ==~ /foo/       // return TRUE
 assert 'foobar' ==~ /foo/    // return FALSE
 ```
 
-It is worth noting that the `~` operator creates a Java `Pattern` object from the given string, while the `=~` operator creates a Java `Matcher` object.
+The `~` operator creates a [Pattern](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/util/regex/Pattern.html) from the given string, while the `=~` operator creates a [Matcher](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/util/regex/Matcher.html):
 
-```groovy
+```nextflow
 x = ~/abc/
 println x.class
 // prints java.util.regex.Pattern
@@ -265,33 +235,39 @@ println y.class
 // prints java.util.regex.Matcher
 ```
 
-Regular expression support is imported from Java. Java's regular expression language and API is documented in the [Pattern](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/util/regex/Pattern.html) class.
-
-You may also be interested in this post: [Groovy: Don't Fear the RegExp](https://web.archive.org/web/20170621185113/http://www.naleid.com/blog/2008/05/19/dont-fear-the-regexp).
+See the linked Java documentation for the available operations for these classes.
 
-#### String replacement
+### String replacement
 
 To replace pattern occurrences in a given string, use the `replaceFirst` and `replaceAll` methods:
 
-```groovy
-x = "colour".replaceFirst(/ou/, "o")
+```nextflow
+def x = "colour".replaceFirst(/ou/, "o")
 println x
 // prints: color
 
-y = "cheesecheese".replaceAll(/cheese/, "nice")
+def y = "cheesecheese".replaceAll(/cheese/, "nice")
 println y
 // prints: nicenice
 ```
 
-#### Capturing groups
+To remove part of a string, simply replace it with a blank string:
+
+```nextflow
+def z = 'Hello World!'.replaceFirst(/(?i)\s+Wo\w+/, '')
+println z
+// prints: Hello!
+```
+
+### Capturing groups
 
 You can match a pattern that includes groups. First create a matcher object with the `=~` operator. Then, you can index the matcher object to find the matches: `matcher[0]` returns a list representing the first match of the regular expression in the string. The first list element is the string that matches the entire regular expression, and the remaining elements are the strings that match each group.
 
 Here's how it works:
 
-```groovy
-programVersion = '2.7.3-beta'
-m = programVersion =~ /(\d+)\.(\d+)\.(\d+)-?(.+)/
+```nextflow
+def programVersion = '2.7.3-beta'
+def m = programVersion =~ /(\d+)\.(\d+)\.(\d+)-?(.+)/
 
 assert m[0] == ['2.7.3-beta', '2', '7', '3', 'beta']
 assert m[0][1] == '2'
@@ -302,9 +278,9 @@ assert m[0][4] == 'beta'
 
 Applying some syntactic sugar, you can do the same in just one line of code:
 
-```groovy
-programVersion = '2.7.3-beta'
-(full, major, minor, patch, flavor) = (programVersion =~ /(\d+)\.(\d+)\.(\d+)-?(.+)/)[0]
+```nextflow
+def programVersion = '2.7.3-beta'
+def (full, major, minor, patch, flavor) = (programVersion =~ /(\d+)\.(\d+)\.(\d+)-?(.+)/)[0]
 
 println full    // 2.7.3-beta
 println major   // 2
@@ -313,110 +289,52 @@ println patch   // 3
 println flavor  // beta
 ```
 
-#### Removing part of a string
-
-You can remove part of a `String` value using a regular expression pattern. The first match found is replaced with an empty String:
-
-```groovy
-// define the regexp pattern
-wordStartsWithGr = ~/(?i)\s+Gr\w+/
-
-// apply and verify the result
-('Hello Groovy world!' - wordStartsWithGr) == 'Hello world!'
-('Hi Grails users' - wordStartsWithGr) == 'Hi users'
-```
-
-Remove the first 5-character word from a string:
-
-```groovy
-assert ('Remove first match of 5 letter word' - ~/\b\w{5}\b/) == 'Remove match of 5 letter word'
-```
-
-Remove the first number with its trailing whitespace from a string:
-
-```groovy
-assert ('Line contains 20 characters' - ~/\d+\s+/) == 'Line contains characters'
-```
-
-### Functions
-
-Functions can be defined using the following syntax:
-
-```groovy
-def <function name> ( arg1, arg, .. ) {
-    <function body>
-}
-```
-
-For example:
-
-```groovy
-def foo() {
-    'Hello world'
-}
-
-def bar(alpha, omega) {
-    alpha + omega
-}
-```
-
-The above snippet defines two simple functions, that can be invoked in the workflow script as `foo()`, which returns `'Hello world'`, and `bar(10, 20)`, which returns the sum of two parameters (`30` in this case).
-
-Functions implicitly return the result of the last statement. Additionally, the `return` keyword can be used to explicitly exit from a function and return the specified value. For example:
-
-```groovy
-def fib( x ) {
-    if( x <= 1 )
-        return x
-
-    fib(x-1) + fib(x-2)
-}
-```
-
 (script-closure)=
 
-### Closures
+## Closures
 
-Briefly, a closure is a block of code that can be passed as an argument to a function. Thus, you can define a chunk of code and then pass it around as if it were a string or an integer.
+A closure is a function that can be used like a regular value. Typically, closures are passed as arguments to *higher-order functions* to express computations in a declarative manner.
 
-More formally, you can create functions that are defined as *first-class objects*.
+For example:
 
-```groovy
-square = { it * it }
+```nextflow
+def square = { v -> v * v }
 ```
 
-The curly brackets around the expression `it * it` tells the script interpreter to treat this expression as code. The `it` identifier is an implicit variable that represents the value that is passed to the function when it is invoked.
+The above example defines a closure, which takes one parameter named `v` and returns the "square" of `v` (`v * v`). The closure is assigned to the variable `square`.
 
-Once compiled the function object is assigned to the variable `square` as any other variable assignments shown previously. Now we can do something like this:
+`square` can now be called like a function:
 
-```groovy
+```nextflow
 println square(9)
 ```
 
-and get the value 81.
+The above example prints `81`.
 
-This is not very interesting until we find that we can pass the function `square` as an argument to other functions or methods. Some built-in functions take a function like this as an argument. One example is the `collect` method on lists:
+The main use case for a closure is as an argument to a higher-order function:
 
-```groovy
+```nextflow
 [ 1, 2, 3, 4 ].collect(square)
 ```
 
-This expression says: Create an array with the values 1, 2, 3 and 4, then call its `collect` method, passing in the closure we defined above. The `collect` method runs through each item in the array, calls the closure on the item, then puts the result in a new array, resulting in:
+The `collect` method of a list applies a mapping function to each value in the list and produces a new list. The above example produces:
 
-```groovy
+```nextflow
 [ 1, 4, 9, 16 ]
 ```
 
-For more methods that you can call with closures as arguments, see the [Groovy GDK documentation](http://docs.groovy-lang.org/latest/html/groovy-jdk/).
+The example can be expressed more concisely as:
+
+```nextflow
+[ 1, 2, 3, 4 ].collect { v -> v * v }
+```
 
-By default, closures take a single parameter called `it`, but you can also create closures with multiple, custom-named parameters. For example, the method `Map.each()` can take a closure with two arguments, to which it binds the `key` and the associated `value` for each key-value pair in the `Map`. Here, we use the obvious variable names `key` and `value` in our closure:
+Another example is the `each` method of a map, which takes a closure with two arguments corresponding to the key and value of each map entry:
 
-```groovy
-printMapClosure = { key, value ->
+```nextflow
+[ "Yue" : "Wu", "Mark" : "Williams", "Sudha" : "Kumari" ].each { key, value ->
     println "$key = $value"
 }
-
-[ "Yue" : "Wu", "Mark" : "Williams", "Sudha" : "Kumari" ].each(printMapClosure)
 ```
 
 Prints:
@@ -427,897 +345,76 @@ Mark = Williams
 Sudha = Kumari
 ```
 
-Closures can also access variables outside of their scope, and they can be used anonymously, that is without assigning them to a variable. Here is an example that demonstrates both of these things:
+Closures can access variables outside of their scope:
 
-```groovy
-myMap = ["China": 1, "India": 2, "USA": 3]
+```nextflow
+def counts = ["China": 1, "India": 2, "USA": 3]
 
-result = 0
-myMap.keySet().each { result += myMap[it] }
+def result = 0
+counts.keySet().each { v ->
+    result += counts[v]
+}
 
 println result
 ```
 
-A closure can also declare local variables that exist only for the lifetime of the closure:
+A closure can also declare local variables that exist only for the lifetime of each closure invocation:
 
-```groovy
-result = 0
-myMap.keySet().each {
-  def count = myMap[it]
-  result += count
+```nextflow
+def result = 0
+myMap.keySet().each { v ->
+    def count = myMap[v]
+    result += count
 }
 ```
 
-:::{warning}
-Local variables should be declared using a qualifier such as `def` or a type name, otherwise they will be interpreted as global variables, which could lead to a {ref}`race condition <cache-global-var-race-condition>`.
-:::
-
-Learn more about closures in the [Groovy documentation](http://groovy-lang.org/closures.html)
-
-### Syntax sugar
-
-Groovy provides several forms of "syntax sugar", or shorthands that can make your code easier to read.
-
-Some programming languages require every statement to be terminated by a semi-colon. In Groovy, semi-colons are optional, but they can still be used to write multiple statements on the same line:
-
-```groovy
-println 'Hello!' ; println 'Hello again!'
-```
-
-When calling a function, the parentheses around the function arguments are optional:
-
-```groovy
-// full syntax
-printf('Hello %s!\n', 'World')
-
-// shorthand
-printf 'Hello %s!\n', 'World'
-```
-
-It is especially useful when calling a function with a closure parameter:
-
-```groovy
-// full syntax
-[1, 2, 3].each({ println it })
-
-// shorthand
-[1, 2, 3].each { println it }
-```
-
-If the last argument is a closure, the closure can be written outside of the parentheses:
-
-```groovy
-// full syntax
-[1, 2, 3].inject('result:', { accum, v -> accum + ' ' + v })
-
-// shorthand
-[1, 2, 3].inject('result:') { accum, v -> accum + ' ' + v }
-```
-
-:::{note}
-In some cases, you might not be able to omit the parentheses because it would be syntactically ambiguous. You can use the `groovysh` REPL console to play around with Groovy and figure out what works.
-:::
-
-(implicit-variables)=
-
-## Implicit variables
-
-### Script implicit variables
-
-The following variables are implicitly defined in the script global execution scope:
-
-`baseDir`
-: :::{deprecated} 20.04.0
-  Use `projectDir` instead
-  :::
-: The directory where the main workflow script is located.
-
-`launchDir`
-: :::{versionadded} 20.04.0
-  :::
-: The directory where the workflow is run.
-
-`moduleDir`
-: :::{versionadded} 20.04.0
-  :::
-: The directory where a module script is located for DSL2 modules or the same as `projectDir` for a non-module script.
-
-`nextflow`
-: Dictionary like object representing nextflow runtime information (see {ref}`metadata-nextflow`).
-
-`params`
-: Dictionary like object holding workflow parameters specifying in the config file or as command line options.
-
-`projectDir`
-: :::{versionadded} 20.04.0
-  :::
-: The directory where the main script is located.
-
-`secrets`
-: :::{versionadded} 24.02.0-edge
-  :::
-: Dictionary like object holding workflow secrets. Read the {ref}`secrets-page` page for more information.
-
-`workDir`
-: The directory where tasks temporary files are created.
-
-`workflow`
-: Dictionary like object representing workflow runtime information (see {ref}`metadata-workflow`).
-
-### Configuration implicit variables
-
-The following variables are implicitly defined in the Nextflow configuration file:
-
-`baseDir`
-: :::{deprecated} 20.04.0
-  Use `projectDir` instead
-  :::
-: The directory where the main workflow script is located.
-
-`launchDir`
-: :::{versionadded} 20.04.0
-  :::
-: The directory where the workflow is run.
-
-`projectDir`
-: :::{versionadded} 20.04.0
-  :::
-: The directory where the main script is located.
-
-### Process implicit variables
-
-The following variables are implicitly defined in the `task` object of each process:
-
-`attempt`
-: The current task attempt
-
-`hash`
-: *Available only in `exec:` blocks*
-: The task unique hash ID
-
-`index`
-: The task index (corresponds to `task_id` in the execution trace)
-
-`name`
-: *Available only in `exec:` blocks*
-: The current task name
-
-`process`
-: The current process name
-
-`workDir`
-: *Available only in `exec:` blocks*
-: The task unique directory
-
-The `task` object also contains the values of all process directives for the given task, which allows you to access these settings at runtime. For examples:
-
-```groovy
-process foo {
-  script:
-  """
-  some_tool --cpus $task.cpus --mem $task.memory
-  """
-}
-```
-
-In the above snippet the `task.cpus` holds the value for the {ref}`cpus directive<process-cpus>` and the `task.memory` the current value for {ref}`memory directive<process-memory>` depending on the actual setting given in the workflow configuration file.
-
-See {ref}`Process directives <process-directives>` for details.
-
-(implicit-functions)=
-
-## Implicit functions
-
-The following functions are available in Nextflow scripts:
-
-`branchCriteria( closure )`
-: Create a branch criteria to use with the {ref}`operator-branch` operator.
-
-`error( message = null )`
-: Throw a script runtime error with an optional error message.
-
-`exit( exitCode = 0, message = null )`
-: :::{deprecated} 22.06.0-edge
-  Use `error()` instead
-  :::
-: Stop the pipeline execution and return an exit code and optional error message.
-
-`file( filePattern, options = [:] )`
-: Get one or more files from a path or glob pattern. Returns a [Path](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/file/Path.html) or list of Paths if there are multiple files. See [Files and I/O](#files-and-io).
-
-`files( filePattern, options = [:] )`
-: Convenience method for `file()` that always returns a list.
-
-`groupKey( key, size )`
-: Create a grouping key to use with the {ref}`operator-grouptuple` operator.
-
-`multiMapCriteria( closure )`
-: Create a multi-map criteria to use with the {ref}`operator-multiMap` operator.
-
-`sendMail( params )`
-: Send an email. See {ref}`mail-page`.
-
-`tuple( collection )`
-: Create a tuple object from the given collection.
-
-`tuple( ... args )`
-: Create a tuple object from the given arguments.
-
-(implicit-classes)=
-
-## Implicit classes
-
-The following classes are imported by default in Nextflow scripts:
-
-- `java.lang.*`
-- `java.util.*`
-- `java.io.*`
-- `java.net.*`
-- `groovy.lang.*`
-- `groovy.util.*`
-- `java.math.BigInteger`
-- `java.math.BigDecimal`
-- `java.nio.file.Path`
-
-Additionally, Nextflow imports several new classes which are described below.
-
-### Channel
-
-The `Channel` class provides the channel factory methods. See {ref}`channel-factory` for more information.
-
-(implicit-classes-duration)=
-
-### Duration
-
-A `Duration` represents some duration of time.
-
-You can create a duration by adding a time unit suffix to an integer, e.g. `1.h`. The following suffixes are available:
-
-| Unit                            | Description  |
-| ------------------------------- | ------------ |
-| `ms`, `milli`, `millis`         | Milliseconds |
-| `s`, `sec`, `second`, `seconds` | Seconds      |
-| `m`, `min`, `minute`, `minutes` | Minutes      |
-| `h`, `hour`, `hours`            | Hours        |
-| `d`, `day`, `days`              | Days         |
-
-You can also create a duration with `Duration.of()`:
-
-```groovy
-// integer value (milliseconds)
-oneSecond = Duration.of(1000)
-
-// simple string value
-oneHour = Duration.of('1h')
-
-// complex string value
-complexDuration = Duration.of('1day 6hours 3minutes 30seconds')
-```
-
-Durations can be compared like numbers, and they support basic arithmetic operations:
-
-```groovy
-a = 1.h
-b = 2.h
-
-assert a < b
-assert a + a == b
-assert b - a == a
-assert a * 2 == b
-assert b / 2 == a
-```
-
-The following methods are available for a `Duration` object:
-
-`getDays()`, `toDays()`
-: Get the duration value in days (rounded down).
-
-`getHours()`, `toHours()`
-: Get the duration value in hours (rounded down).
-
-`getMillis()`, `toMillis()`
-: Get the duration value in milliseconds.
-
-`getMinutes()`, `toMinutes()`
-: Get the duration value in minutes (rounded down).
-
-`getSeconds()`, `toSeconds()`
-: Get the duration value in seconds (rounded down).
-
-(implicit-classes-memoryunit)=
-
-### MemoryUnit
-
-A `MemoryUnit` represents a quantity of bytes.
-
-You can create a memory unit by adding a unit suffix to an integer, e.g. `1.GB`. The following suffixes are available:
-
-| Unit | Description |
-| ---- | ----------- |
-| `B`  | Bytes       |
-| `KB` | Kilobytes   |
-| `MB` | Megabytes   |
-| `GB` | Gigabytes   |
-| `TB` | Terabytes   |
-| `PB` | Petabytes   |
-| `EB` | Exabytes    |
-| `ZB` | Zettabytes  |
-
-:::{note}
-Technically speaking, a kilobyte is equal to 1000 bytes, whereas 1024 bytes is called a "kibibyte" and abbreviated as "KiB", and so on for the other units. In practice, however, kilobyte is commonly understood to mean 1024 bytes, and Nextflow follows this convention in its implementation as well as this documentation.
-:::
-
-You can also create a memory unit with `MemoryUnit.of()`:
-
-```groovy
-// integer value (bytes)
-oneKilobyte = MemoryUnit.of(1024)
-
-// string value
-oneGigabyte = MemoryUnit.of('1 GB')
-```
-
-Memory units can be compared like numbers, and they support basic arithmetic operations:
-
-```groovy
-a = 1.GB
-b = 2.GB
-
-assert a < b
-assert a + a == b
-assert b - a == a
-assert a * 2 == b
-assert b / 2 == a
-```
-
-The following methods are available for a `MemoryUnit` object:
-
-`getBytes()`, `toBytes()`
-: Get the memory value in bytes (B).
-
-`getGiga()`, `toGiga()`
-: Get the memory value in gigabytes (rounded down), where 1 GB = 1024 MB.
-
-`getKilo()`, `toKilo()`
-: Get the memory value in kilobytes (rounded down), where 1 KB = 1024 B.
-
-`getMega()`, `toMega()`
-: Get the memory value in megabytes (rounded down), where 1 MB = 1024 KB.
-
-`toUnit( unit )`
-: Get the memory value in terms of a given unit (rounded down). The unit can be one of: `'B'`, `'KB'`, `'MB'`, `'GB'`, `'TB'`, `'PB'`, `'EB'`, `'ZB'`.
-
-### ValueObject
-
-`ValueObject` is an AST transformation for classes and enums, which simply combines [AutoClone](http://docs.groovy-lang.org/latest/html/gapi/groovy/transform/AutoClone.html) and [Immutable](https://docs.groovy-lang.org/latest/html/gapi/groovy/transform/Immutable.html). It is useful for defining custom "record" types.
-
-(script-file-io)=
-
-## Files and I/O
-
-### Opening files
-
-To access and work with files, use the `file()` method, which returns a file system object given a file path string:
-
-```groovy
-myFile = file('some/path/to/my_file.file')
-```
-
-The `file()` method can reference both files and directories, depending on what the string path refers to in the file system.
-
-When using the wildcard characters `*`, `?`, `[]` and `{}`, the argument is interpreted as a [glob](http://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob) path matcher and the `file()` method returns a list object holding the paths of files whose names match the specified pattern, or an empty list if no match is found:
+While the `each` method is a convenient way to iterate through a collection and build up some result, a more idiomatic way to do this is to use the `inject` method:
 
-```groovy
-listOfFiles = file('some/path/*.fa')
+```nextflow
+def result = counts.values().inject { sum, v -> sum + v }
 ```
 
-:::{note}
-The `file()` method does not return a list if only one file is matched. Use the `files()` method to always return a list.
-:::
+This way, the closure is fully "self-contained" because it doesn't access or mutate any variables outside of its scope.
 
 :::{note}
-A double asterisk (`**`) in a glob pattern works like `*` but also searches through subdirectories.
-:::
-
-By default, wildcard characters do not match directories or hidden files. For example, if you want to include hidden files in the result list, enable the `hidden` option:
-
-```groovy
-listWithHidden = file('some/path/*.fa', hidden: true)
-```
-
-:::{note}
-To compose paths, instead of string interpolation, use the `resolve()` method or the `/` operator:
-
-```groovy
-def dir = file('s3://bucket/some/data/path')
-def sample1 = dir.resolve('sample.bam')         // correct
-def sample2 = dir / 'sample.bam'
-def sample3 = file("$dir/sample.bam")           // correct (but verbose)
-def sample4 = "$dir/sample.bam"                 // incorrect
-```
-:::
-
-The following options are available:
-
-`checkIfExists`
-: When `true`, throws an exception if the specified path does not exist in the file system (default: `false`)
-
-`followLinks`
-: When `true`, follows symbolic links when traversing a directory tree, otherwise treats them as files (default: `true`)
-
-`glob`
-: When `true`, interprets characters `*`, `?`, `[]` and `{}` as glob wildcards, otherwise handles them as normal characters (default: `true`)
-
-`hidden`
-: When `true`, includes hidden files in the resulting paths (default: `false`)
-
-`maxDepth`
-: Maximum number of directory levels to visit (default: *no limit*)
-
-`type`
-: Type of paths returned, can be `'file'`, `'dir'` or `'any'` (default: `'file'`)
-
-See also: {ref}`Channel.fromPath <channel-path>`.
-
-### Getting file attributes
-
-The `file()` method returns a [Path](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/file/Path.html), so any method defined for Path can also be used in a Nextflow script.
-
-Additionally, the following methods are also defined for Paths in Nextflow:
-
-`exists()`
-: Returns `true` if the file exists.
-
-`getBaseName()`
-: Gets the file name without its extension, e.g. `/some/path/file.tar.gz` -> `file.tar`.
-
-`getExtension()`
-: Gets the file extension, e.g. `/some/path/file.txt` -> `txt`.
-
-`getName()`
-: Gets the file name, e.g. `/some/path/file.txt` -> `file.txt`.
-
-`getSimpleName()`
-: Gets the file name without any extension, e.g. `/some/path/file.tar.gz` -> `file`.
-
-`getParent()`
-: Gets the file parent path, e.g. `/some/path/file.txt` -> `/some/path`.
-
-`getScheme()`
-: Gets the file URI scheme, e.g. `s3://some-bucket/foo.txt` -> `s3`.
-
-`isDirectory()`
-: Returns `true` if the file is a directory.
-
-`isEmpty()`
-: Returns `true` if the file is empty or does not exist.
-
-`isFile()`
-: Returns `true` if it is a regular file (i.e. not a directory).
-
-`isHidden()`
-: Returns `true` if the file is hidden.
-
-`isLink()`
-: Returns `true` if the file is a symbolic link.
-
-`lastModified()`
-: Returns the file last modified timestamp in Unix time (i.e. milliseconds since January 1, 1970).
-
-`size()`
-: Gets the file size in bytes.
-
-`toUriString()`
-: Gets the file path along with the protocol scheme:
-  ```groovy
-  def ref = file('s3://some-bucket/foo.txt')
-
-  assert ref.toString() == '/some-bucket/foo.txt'
-  assert "$ref" == '/some-bucket/foo.txt'
-  assert ref.toUriString() == 's3://some-bucket/foo.txt'
-  ```
-
-:::{tip}
-In Groovy, any method that looks like `get*()` can also be accessed as a field. For example, `myFile.getName()` is equivalent to `myFile.name`, `myFile.getBaseName()` is equivalent to `myFile.baseName`, and so on.
-:::
-
-### Reading and writing
+When a closure takes a single parameter, the parameter can be omitted, in which case the implicit `it` parameter will be used:
 
-#### Reading and writing an entire file
-
-Given a file variable, created with the `file()` method as shown previously, reading a file is as easy as getting the file's `text` property, which returns the file content as a string:
-
-```groovy
-print myFile.text
-```
-
-Similarly, you can save a string to a file by assigning it to the file's `text` property:
-
-```groovy
-myFile.text = 'Hello world!'
-```
-
-Binary data can managed in the same way, just using the file property `bytes` instead of `text`. Thus, the following example reads the file and returns its content as a byte array:
-
-```groovy
-binaryContent = myFile.bytes
-```
-
-Or you can save a byte array to a file:
-
-```groovy
-myFile.bytes = binaryContent
+```nextflow
+[1, 2, 3].each { println it }
 ```
-
-:::{note}
-The above assignment overwrites any existing file contents, and implicitly creates the file if it doesn't exist.
-:::
-
-:::{warning}
-The above methods read and write the **entire** file contents at once, in a single variable or buffer. For this reason, when dealing with large files it is recommended that you use a more memory efficient approach, such as reading/writing a file line by line or using a fixed size buffer.
 :::
 
-#### Appending to a file
+## Script definitions
 
-In order to append a string value to a file without erasing existing content, you can use the `append()` method:
+So far, we have been focusing on the basic building blocks of Nextflow code, like variables, lists, strings, and closures.
 
-```groovy
-myFile.append('Add this line\n')
-```
+In practice, however, Nextflow scripts are composed of *workflows*, *processes*, and *functions* (collectively known as *definitions*), and can *include*  definitions from other scripts.
 
-Or use the left shift operator, a more idiomatic way to append text content to a file:
+To transition a code snippet into a proper workflow script, simply wrap it in a `workflow` block:
 
-```groovy
-myFile << 'Add a line more\n'
-```
-
-#### Reading a file line by line
-
-In order to read a text file line by line you can use the method `readLines()` provided by the file object, which returns the file content as a list of strings:
-
-```groovy
-myFile = file('some/my_file.txt')
-allLines = myFile.readLines()
-for( line : allLines ) {
-    println line
+```nextflow
+workflow {
+    println 'Hello!'
 }
 ```
 
-This can also be written in a more idiomatic syntax:
+This block is called the *entry workflow*. It serves as the entrypoint when the script is executed. A script can only have one entry workflow. Whenever a script contains only simple statements like `println 'Hello!'`, Nextflow simply treats it as an entry workflow.
 
-```groovy
-file('some/my_file.txt')
-    .readLines()
-    .each { println it }
-```
+You can also break up code into functions, for example:
 
-:::{warning}
-The method `readLines()` reads the **entire** file at once and returns a list containing all the lines. For this reason, do not use it to read big files.
-:::
-
-To process a big file, use the method `eachLine()`, which reads only a single line at a time into memory:
-
-```groovy
-count = 0
-myFile.eachLine { str ->
-    println "line ${count++}: $str"
+```nextflow
+def sayHello() {
+    println 'Hello!'
 }
-```
-
-#### Advanced file reading
 
-The classes `Reader` and `InputStream` provide fine-grained control for reading text and binary files, respectively.
-
-The method `newReader()` creates a [Reader](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/Reader.html) object for the given file that allows you to read the content as single characters, lines or arrays of characters:
-
-```groovy
-myReader = myFile.newReader()
-String line
-while( line = myReader.readLine() ) {
-    println line
+def add(a, b) {
+    a + b
 }
-myReader.close()
-```
 
-The method `withReader()` works similarly, but automatically calls the `close()` method for you when you have finished processing the file. So, the previous example can be written more simply as:
-
-```groovy
-myFile.withReader {
-    String line
-    while( line = it.readLine() ) {
-        println line
-    }
+workflow {
+    sayHello()
+    println "2 + 2 = ${add(2, 2)}!"
 }
 ```
 
-The methods `newInputStream()` and `withInputStream()` work similarly. The main difference is that they create an [InputStream](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/InputStream.html) object useful for writing binary data.
-
-The following methods are useful for reading files:
-
-`eachByte( closure )`
-: Iterates over the file byte by byte, applying the specified {ref}`closure <script-closure>`.
-
-`eachLine( closure )`
-: Iterates over the file line by line, applying the specified {ref}`closure <script-closure>`.
-
-`getBytes()`
-: Returns the file content as a byte array.
-
-`getText()`
-: Returns the file content as a string value.
-
-`newInputStream()`
-: Returns an [InputStream](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/InputStream.html) object to read a binary file.
-
-`newReader()`
-: Returns a [Reader](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/Reader.html) object to read a text file.
-
-`readLines()`
-: Reads the file line by line and returns the content as a list of strings.
-
-`withInputStream( closure )`
-: Opens a file for reading and lets you access it with an [InputStream](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/InputStream.html) object.
-
-`withReader( closure )`
-: Opens a file for reading and lets you access it with a [Reader](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/Reader.html) object.
-
-#### Advanced file writing
-
-The `Writer` and `OutputStream` classes provide fine-grained control for writing text and binary files, respectively, including low-level operations for single characters or bytes, and support for big files.
-
-For example, given two file objects `sourceFile` and `targetFile`, the following code copies the first file's content into the second file, replacing all `U` characters with `X`:
-
-```groovy
-sourceFile.withReader { source ->
-    targetFile.withWriter { target ->
-        String line
-        while( line=source.readLine() ) {
-            target << line.replaceAll('U','X')
-        }
-    }
-}
-```
-
-The following methods are available for writing to files:
-
-`append( text )`
-: Appends a string value to a file without replacing existing content.
-
-`newOutputStream()`
-: Creates an [OutputStream](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/OutputStream.html) object that allows you to write binary data to a file.
-
-`newPrintWriter()`
-: Creates a [PrintWriter](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/PrintWriter.html) object that allows you to write formatted text to a file.
-
-`newWriter()`
-: Creates a [Writer](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/Writer.html) object that allows you to save text data to a file.
-
-`setBytes( bytes )`
-: Writes a byte array to a file. Equivalent to setting the `bytes` property.
-
-`setText( text )`
-: Writes a string value to a file. Equivalent to setting the `text` property.
-
-`withOutputStream( closure )`
-: Applies the specified closure to an [OutputStream](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/OutputStream.html) object, closing it when finished.
-
-`withPrintWriter( closure )`
-: Applies the specified closure to a [PrintWriter](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/PrintWriter.html) object, closing it when finished.
-
-`withWriter( closure )`
-: Applies the specified closure to a [Writer](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/Writer.html) object, closing it when finished.
-
-`write( text )`
-: Writes a string to a file, replacing any existing content.
-
-### Filesystem operations
-
-The following methods are available for manipulating files and directories in a filesystem:
-
-`copyTo( target )`
-: Copies a source file or directory to a target file or directory.
-
-: *When copying a file to another file:* if the target file already exists, it will be replaced.
-
-  ```groovy
-  file('/some/path/my_file.txt').copyTo('/another/path/new_file.txt')
-  ```
-
-: *When copying a file to a directory:* the file will be copied into the directory, replacing any file with the same name.
-
-  ```groovy
-  file('/some/path/my_file.txt').copyTo('/another/path')
-  ```
-
-: *When copying a directory to another directory:* if the target directory already exists, the source directory will be copied into the target directory, replacing any sub-directory with the same name. If the target path does not exist, it will be created automatically.
-
-  ```groovy
-  file('/any/dir_a').moveTo('/any/dir_b')
-  ```
-
-  The result of the above example depends on the existence of the target directory. If the target directory exists, the source is moved into the target directory, resulting in the path `/any/dir_b/dir_a`. If the target directory does not exist, the source is just renamed to the target name, resulting in the path `/any/dir_b`.
-
-: :::{note}
-  The `copyTo()` method follows the semantics of the Linux command `cp -r <source> <target>`, with the following caveat: while Linux tools often treat paths ending with a slash (e.g. `/some/path/name/`) as directories, and those not (e.g. `/some/path/name`) as regular files, Nextflow (due to its use of the Java files API) views both of these paths as the same file system object. If the path exists, it is handled according to its actual type (i.e. as a regular file or as a directory). If the path does not exist, it is treated as a regular file, with any missing parent directories created automatically.
-  :::
-
-`delete()`
-: Deletes the file or directory at the given path, returning `true` if the operation succeeds, and `false` otherwise:
-
-  ```groovy
-  myFile = file('some/file.txt')
-  result = myFile.delete()
-  println result ? "OK" : "Cannot delete: $myFile"
-  ```
-
-  If a directory is not empty, it will not be deleted and `delete()` will return `false`.
-
-`deleteDir()`
-: Deletes a directory and all of its contents.
-
-  ```groovy
-  file('any/path').deleteDir()
-  ```
-
-`getPermissions()`
-: Returns a file's permissions using the [symbolic notation](http://en.wikipedia.org/wiki/File_system_permissions#Symbolic_notation), e.g. `'rw-rw-r--'`.
-
-`list()`
-: Returns the first-level elements (files and directories) of a directory as a list of strings.
-
-`listFiles()`
-: Returns the first-level elements (files and directories) of a directory as a list of Paths.
-
-`mkdir()`
-: Creates a directory at the given path, returning `true` if the directory is created successfully, and `false` otherwise:
-
-  ```groovy
-  myDir = file('any/path')
-  result = myDir.mkdir()
-  println result ? "OK" : "Cannot create directory: $myDir"
-  ```
-
-  If the parent directories do not exist, the directory will not be created and `mkdir()` will return `false`.
-
-`mkdirs()`
-: Creates a directory at the given path, including any nonexistent parent directories:
-
-  ```groovy
-  file('any/path').mkdirs()
-  ```
-
-`mklink( linkName, options = [:] )`
-: Creates a *filesystem link* to a given path:
-
-  ```groovy
-  myFile = file('/some/path/file.txt')
-  myFile.mklink('/user/name/link-to-file.txt')
-  ```
-
-  Available options:
-
-  `hard`
-  : When `true`, creates a *hard* link, otherwise creates a *soft* (aka *symbolic*) link (default: `false`).
-
-  `overwrite`
-  : When `true`, overwrites any existing file with the same name, otherwise throws a [FileAlreadyExistsException](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/file/FileAlreadyExistsException.html) (default: `false`).
-
-`moveTo( target )`
-: Moves a source file or directory to a target file or directory. Follows the same semantics as `copyTo()`.
-
-`renameTo( target )`
-: Rename a file or directory:
-
-  ```groovy
-  file('my_file.txt').renameTo('new_file_name.txt')
-  ```
-
-`setPermissions( permissions )`
-: Sets a file's permissions using the [symbolic notation](http://en.wikipedia.org/wiki/File_system_permissions#Symbolic_notation):
-
-  ```groovy
-  myFile.setPermissions('rwxr-xr-x')
-  ```
-
-`setPermissions( owner, group, other )`
-: Sets a file's permissions using the [numeric notation](http://en.wikipedia.org/wiki/File_system_permissions#Numeric_notation), i.e. as three digits representing the **owner**, **group**, and **other** permissions:
-
-  ```groovy
-  myFile.setPermissions(7,5,5)
-  ```
-
-#### Listing directories
-
-The simplest way to list a directory is to use `list()` or `listFiles()`, which return a collection of first-level elements (files and directories) of a directory:
-
-```groovy
-for( def file : file('any/path').list() ) {
-    println file
-}
-```
-
-Additionally, the `eachFile()` method allows you to iterate through the first-level elements only (just like `listFiles()`). As with other `each*()` methods, `eachFile()` takes a closure as a parameter:
-
-```groovy
-myDir.eachFile { item ->
-    if( item.isFile() ) {
-        println "${item.getName()} - size: ${item.size()}"
-    }
-    else if( item.isDirectory() ) {
-        println "${item.getName()} - DIR"
-    }
-}
-```
-
-The following methods are available for listing and traversing directories:
-
-`eachDir( closure )`
-: Iterates through first-level directories only. [Read more](http://docs.groovy-lang.org/latest/html/groovy-jdk/java/io/File.html#eachDir(groovy.lang.Closure))
-
-`eachDirMatch( nameFilter, closure )`
-: Iterates through directories whose names match the given filter. [Read more](http://docs.groovy-lang.org/latest/html/groovy-jdk/java/io/File.html#eachDirMatch(java.lang.Object,%20groovy.lang.Closure))
-
-`eachDirRecurse( closure )`
-: Iterates through directories depth-first (regular files are ignored). [Read more](http://docs.groovy-lang.org/latest/html/groovy-jdk/java/io/File.html#eachDirRecurse(groovy.lang.Closure))
-
-`eachFile( closure )`
-: Iterates through first-level files and directories. [Read more](http://docs.groovy-lang.org/latest/html/groovy-jdk/java/io/File.html#eachFile(groovy.lang.Closure))
-
-`eachFileMatch( nameFilter, closure )`
-: Iterates through files and directories whose names match the given filter. [Read more](http://docs.groovy-lang.org/latest/html/groovy-jdk/java/io/File.html#eachFileMatch(java.lang.Object,%20groovy.lang.Closure))
-
-`eachFileRecurse( closure )`
-: Iterates through files and directories depth-first. [Read more](http://docs.groovy-lang.org/latest/html/groovy-jdk/java/io/File.html#eachFileRecurse(groovy.lang.Closure))
-
-See also: {ref}`Channel.fromPath <channel-path>`.
-
-### Fetching HTTP/FTP files
-
-Nextflow integrates seamlessly with the HTTP(S) and FTP protocols for handling remote resources the same as local files. Simply specify the resource URL when opening the file:
-
-```groovy
-pdb = file('http://files.rcsb.org/header/5FID.pdb')
-```
-
-Then, you can access it as a local file as described previously:
-
-```groovy
-println pdb.text
-```
-
-The above one-liner prints the content of the remote PDB file. Previous sections provide code examples showing how to stream or copy the content of files.
-
-:::{note}
-Write and list operations are not supported for HTTP(S) and FTP files.
-:::
-
-### Splitting and counting records
-
-The following methods are defined for Paths for splitting and counting records:
-
-`countFasta()`
-: Counts the number of records in a [FASTA](https://en.wikipedia.org/wiki/FASTA_format) file. See the {ref}`operator-splitfasta` operator for available options.
-
-`countFastq()`
-: Counts the number of records in a [FASTQ](https://en.wikipedia.org/wiki/FASTQ_format) file. See the {ref}`operator-splitfastq` operator for available options.
-
-`countJson()`
-: Counts the number of records in a JSON file. See the {ref}`operator-splitjson` operator for available options.
-
-`countLines()`
-: Counts the number of lines in a text file. See the {ref}`operator-splittext` operator for available options.
-
-`splitCsv()`
-: Splits a CSV file into a list of records. See the {ref}`operator-splitcsv` operator for available options.
-
-`splitFasta()`
-: Splits a [FASTA](https://en.wikipedia.org/wiki/FASTA_format) file into a list of records. See the {ref}`operator-splitfasta` operator for available options.
-
-`splitFastq()`
-: Splits a [FASTQ](https://en.wikipedia.org/wiki/FASTQ_format) file into a list of records. See the {ref}`operator-splitfastq` operator for available options.
-
-`splitJson()`
-: Splits a JSON file into a list of records. See the {ref}`operator-splitjson` operator for available options.
-
-`splitText()`
-: Splits a text file into a list of lines. See the {ref}`operator-splittext` operator for available options.
+See {ref}`workflow-page`, {ref}`process-page`, and {ref}`module-page`  for more information about how to use these features in your Nextflow scripts.
diff --git a/docs/secrets.md b/docs/secrets.md
index e75368271f..b20ce13134 100644
--- a/docs/secrets.md
+++ b/docs/secrets.md
@@ -51,11 +51,12 @@ Secrets **cannot** be assigned to pipeline parameters.
 
 Secrets can be access by pipeline processes by using the `secret` directive. For example:
 
-```groovy
+```nextflow
 process someJob {
     secret 'MY_ACCESS_KEY'
     secret 'MY_SECRET_KEY'
 
+    script:
     """
     your_command --access \$MY_ACCESS_KEY --secret \$MY_SECRET_KEY
     """
@@ -79,7 +80,7 @@ This feature is only available when using the local or grid executors (Slurm, Gr
 
 Secrets can be accessed in the pipeline script using the `secrets` variable. For example:
 
-```groovy
+```nextflow
 workflow.onComplete {
     println("The secret is: ${secrets.MY_SECRET}")
 }
diff --git a/docs/sharing.md b/docs/sharing.md
index 2db5b9b527..61a840e9f8 100644
--- a/docs/sharing.md
+++ b/docs/sharing.md
@@ -1,398 +1,22 @@
 (sharing-page)=
 
-# Pipeline sharing
+# Sharing pipelines
 
-Nextflow seamlessly integrates with [BitBucket](http://bitbucket.org/) [^id2], [GitHub](http://github.com), and [GitLab](http://gitlab.com) hosted code repositories and sharing platforms. This feature allows you to manage your project code in a more consistent manner or use other people's Nextflow pipelines, published through BitBucket/GitHub/GitLab, in a quick and transparent way.
-
-## How it works
-
-When you launch a script execution with Nextflow, it will look for a file with the pipeline name you've specified. If that file does not exist, it will look for a public repository with the same name on GitHub (unless otherwise specified). If it is found, the repository is automatically downloaded to your computer and executed. This repository is stored in the Nextflow home directory, that is by default the `$HOME/.nextflow` path, and thus will be reused for any further executions.
-
-## Running a pipeline
-
-To launch the execution of a pipeline project, hosted in a remote code repository, you simply need to specify its qualified name or the repository URL after the `run` command. The qualified name is formed by two parts: the `owner` name and the `repository` name separated by a `/` character.
-
-In other words if a Nextflow project is hosted, for example, in a GitHub repository at the address `http://github.com/foo/bar`, it can be executed by entering the following command in your shell terminal:
-
-```bash
-nextflow run foo/bar
-```
-
-or using the project URL:
-
-```bash
-nextflow run http://github.com/foo/bar
-```
-
-:::{note}
-In the first case, if your project is hosted on a service other than GitHub, you will need to specify this hosting service in the command line by using the `-hub` option. For example `-hub bitbucket` or `-hub gitlab`. In the second case, i.e. when using the project URL as name, the `-hub` option is not needed.
-:::
-
-You can try this feature out by simply entering the following command in your shell terminal:
-
-```bash
-nextflow run nextflow-io/hello
-```
-
-It will download a trivial `Hello` example from the repository published at the following address <http://github.com/nextflow-io/hello> and execute it in your computer.
-
-If the `owner` part in the pipeline name is omitted, Nextflow will look for a pipeline between the ones you have already executed having a name that matches the name specified. If none is found it will try to download it using the `organisation` name defined by the environment variable `NXF_ORG` (which by default is `nextflow-io`).
-
-:::{tip}
-To access a private repository, specify the access credentials by using the `-user` command line option, then the program will ask you to enter the password interactively. Private repository access credentials can also be defined in the [SCM configuration file](#scm-configuration-file)(#s.
-:::
-
-## Handling revisions
-
-Any Git branch, tag or commit ID defined in a project repository, can be used to specify the revision that you want to execute when launching a pipeline by adding the `-r` option to the run command line. So for example you could enter:
-
-```bash
-nextflow run nextflow-io/hello -r mybranch
-```
-
-or
-
-```bash
-nextflow run nextflow-io/hello -r v1.1
-```
-
-It will execute two different project revisions corresponding to the Git tag/branch having that names.
-
-## Commands to manage projects
-
-The following commands allows you to perform some basic operations that can be used to manage your projects.
+Nextflow seamlessly integrates with popular Git providers, including [BitBucket](http://bitbucket.org/), [GitHub](http://github.com), and [GitLab](http://gitlab.com) for managing Nextflow pipelines as version-controlled Git repositories. This feature allows you to easily use other people's Nextflow pipelines and publish your own pipelines.
 
 :::{note}
 Nextflow is not meant to completely replace the [Git](https://git-scm.com/) tool. You may still need `git` to create new repositories or commit changes, etc.
 :::
 
-### Listing available projects
-
-The `list` command allows you to list all the projects you have downloaded in your computer. For example:
-
-```bash
-nextflow list
-```
-
-This prints a list similar to the following one:
-
-```
-cbcrg/ampa-nf
-cbcrg/piper-nf
-nextflow-io/hello
-nextflow-io/examples
-```
-
-### Showing project information
-
-By using the `info` command you can show information from a downloaded project. For example:
-
-```console
-$ nextflow info hello
-project name: nextflow-io/hello
-repository  : http://github.com/nextflow-io/hello
-local path  : $HOME/.nextflow/assets/nextflow-io/hello
-main script : main.nf
-revisions   :
-* master (default)
-  mybranch
-  v1.1 [t]
-  v1.2 [t]
-```
-
-Starting from the top it shows: 1) the project name; 2) the Git repository URL; 3) the local folder where the project has been downloaded; 4) the script that is executed when launched; 5) the list of available revisions i.e. branches and tags. Tags are marked with a `[t]` on the right, the current checked-out revision is marked with a `*` on the left.
-
-### Pulling or updating a project
-
-The `pull` command allows you to download a project from a GitHub repository or to update it if that repository has already been downloaded. For example:
-
-```bash
-nextflow pull nextflow-io/examples
-```
-
-Alternatively, you can use the repository URL as the name of the project to pull:
-
-```bash
-nextflow pull https://github.com/nextflow-io/examples
-```
-
-Downloaded pipeline projects are stored in the folder `$HOME/.nextflow/assets` in your computer.
-
-### Viewing the project code
-
-The `view` command allows you to quickly show the content of the pipeline script you have downloaded. For example:
-
-```bash
-nextflow view nextflow-io/hello
-```
-
-By adding the `-l` option to the example above it will list the content of the repository.
-
-### Cloning a project into a folder
-
-The `clone` command allows you to copy a Nextflow pipeline project to a directory of your choice. For example:
-
-```bash
-nextflow clone nextflow-io/hello target-dir
-```
-
-If the destination directory is omitted the specified project is cloned to a directory with the same name as the pipeline base name (e.g. `hello`) in the current folder.
-
-The clone command can be used to inspect or modify the source code of a pipeline project. You can eventually commit and push back your changes by using the usual Git/GitHub workflow.
-
-### Deleting a downloaded project
-
-Downloaded pipelines can be deleted by using the `drop` command, as shown below:
-
-```bash
-nextflow drop nextflow-io/hello
-```
-
-(sharing-scm-file)=
-
-## SCM configuration file
-
-The file `$HOME/.nextflow/scm` allows you to centralise the security credentials required to access private project repositories on Bitbucket, GitHub and GitLab source code management (SCM) platforms or to manage the configuration properties of private server installations (of the same platforms).
-
-The configuration properties for each SCM platform are defined inside the `providers` section, properties for the same provider are grouped together with a common name and delimited with curly brackets as in this example:
-
-```groovy
-providers {
-    <provider-name> {
-        property = value
-        // ...
-    }
-}
-```
-
-In the above template replace `<provider-name>` with one of the "default" servers (i.e. `bitbucket`, `github` or `gitlab`) or a custom identifier representing a private SCM server installation.
-
-:::{versionadded} 20.10.0
-A custom location for the SCM file can be specified using the `NXF_SCM_FILE` environment variable.
-:::
-
-The following configuration properties are supported for each provider configuration:
-
-`providers.<provider>.user`
-: User name required to access private repositories on the SCM server.
-
-`providers.<provider>.password`
-: User password required to access private repositories on the SCM server.
-
-`providers.<provider>.token`
-: *Required only for private Gitlab servers*
-: Private API access token.
-
-`providers.<provider>.platform`
-: *Required only for private SCM servers*
-: SCM platform name, either: `github`, `gitlab` or `bitbucket`.
-
-`providers.<provider>.server`
-: *Required only for private SCM servers*
-: SCM server name including the protocol prefix e.g. `https://github.com`.
-
-`providers.<provider>.endpoint`
-: *Required only for private SCM servers*
-: SCM API `endpoint` URL e.g. `https://api.github.com` (default: the same as `providers.<provider>.server`).
-
-## SCM providers
-
-### BitBucket credentials
-
-Create a `bitbucket` entry in the [SCM configuration file](#scm-configuration-file) specifying your user name and app password, as shown below:
-
-```groovy
-providers {
-    bitbucket {
-        user = 'me'
-        password = 'my-secret'
-    }
-}
-```
-
-:::{note}
-App passwords are substitute passwords for a user account which you can use for scripts and integrating tools in order to avoid putting your real password into configuration files. Learn more at [this link](https://support.atlassian.com/bitbucket-cloud/docs/app-passwords/).
-:::
-
-### BitBucket Server credentials
-
-[BitBucket Server](https://confluence.atlassian.com/bitbucketserver) is a self-hosted Git repository and management platform.
-
-:::{note}
-BitBucket Server uses a different API from the [BitBucket](https://bitbucket.org/) cloud service. Make sure to use the right configuration whether you are using the cloud service or a self-hosted installation.
-:::
-
-To access your local BitBucket Server create an entry in the [SCM configuration file](#scm-configuration-file) specifying as shown below:
-
-```groovy
-providers {
-    mybitbucket {
-        platform = 'bitbucketserver'
-        server = 'https://your.bitbucket.host.com'
-        endpoint = 'https://your.bitbucket.host.com'
-        user = 'your-user'
-        password = 'your-password or your-token'
-    }
-}
-```
-
-### GitHub credentials
-
-Create a `github` entry in the [SCM configuration file](#scm-configuration-file) specifying your user name and access token as shown below:
-
-```groovy
-providers {
-    github {
-        user = 'your-user-name'
-        password = 'your-personal-access-token'
-    }
-}
-```
-
-GitHub requires the use of a personal access token (PAT) in place of a password when accessing APIs. Learn more about PAT and how to create it at [this link](https://docs.github.com/en/github/authenticating-to-github/keeping-your-account-and-data-secure/creating-a-personal-access-token).
-
-:::{versionadded} 23.01.0-edge
-Nextflow automatically uses the `GITHUB_TOKEN` environment variable to authenticate access to the GitHub repository if no credentials are provided via the `scm` file. This is useful especially when accessing pipeline code from a GitHub Action. Read more about the token authentication in the [GitHub documentation](https://docs.github.com/en/actions/security-guides/automatic-token-authentication).
-:::
-
-### GitLab credentials
-
-Create a `gitlab` entry in the [SCM configuration file](#scm-configuration-file) specifying the user name, password and your API access token that can be found in your GitLab [account page](https://gitlab.com/profile/account) (sign in required). For example:
-
-```groovy
-providers {
-    gitlab {
-        user = 'me'
-        password = 'my-secret'
-        token = 'YgpR8m7viH_ZYnC8YSe8'
-    }
-}
-```
-
-:::{tip}
-The GitLab *token* string can be used as the `password` value in the above setting. When doing that the `token` field can be omitted.
-:::
-
-### Gitea credentials
-
-[Gitea](https://gitea.io) is a Git repository server with GitHub-like GUI access. Since Gitea installation is quite easy, it is suitable for building a private development environment in your network. To access your Gitea server, you have to provide all the credential information below:
-
-```groovy
-providers {
-    mygitea {
-        server = 'http://your-domain.org/gitea'
-        endpoint = 'http://your-domain.org/gitea/api/v1'
-        platform = 'gitea'
-        user = 'your-user'
-        password = 'your-password'
-        token = 'your-api-token'
-    }
-}
-```
-
-See [Gitea documentation](https://docs.gitea.io/en-us/api-usage/) about how to enable API access on your server and how to issue a token.
-
-### Azure Repos credentials
-
-Nextflow has a builtin support for [Azure Repos](https://azure.microsoft.com/en-us/services/devops/repos/), a Git source code management service hosted in the Azure cloud. To access your Azure Repos with Nextflow provide the repository credentials using the configuration snippet shown below:
-
-```groovy
-providers {
-    azurerepos {
-        user = 'your-user-name'
-        password = 'your-personal-access-token'
-    }
-}
-```
-
-:::{tip}
-The Personal access token can be generated in the repository `Clone Repository` dialog.
-:::
-
-(aws-codecommit)=
+## Git configuration
 
-### AWS CodeCommit credentials
+You can configure your credentials for various Git providers in the Git configuration file, located at `$HOME/.nextflow/scm`. See {ref}`git-page` for more information.
 
-:::{versionadded} 22.06.0-edge
-:::
+## Using a local repository
 
-Nextflow supports [AWS CodeCommit](https://aws.amazon.com/codecommit/) as a Git provider to access and to share pipelines code.
+Nextflow can work with repositories stored in a local or shared file system. The repository must be created as a [bare repository](https://mijingo.com/blog/what-is-a-bare-git-repository).
 
-To access your project hosted on AWS CodeCommit with Nextflow provide the repository credentials using the configuration snippet shown below:
-
-```groovy
-providers {
-    my_aws_repo {
-        platform = 'codecommit'
-        user = '<AWS ACCESS KEY>'
-        password = '<AWS SECRET KEY>'
-    }
-}
-```
-
-In the above snippet replace `<AWS ACCESS KEY>` and `<AWS SECRET KEY>` with your AWS credentials, and `my_aws_repo` with a name of your choice.
-
-:::{tip}
-The `user` and `password` are optional settings, if omitted the [AWS default credentials provider chain](https://docs.aws.amazon.com/sdk-for-java/v1/developer-guide/credentials.html) is used.
-:::
-
-Then the pipeline can be accessed with Nextflow as shown below:
-
-```bash
-nextflow run https://git-codecommit.eu-west-1.amazonaws.com/v1/repos/my-repo
-```
-
-In the above example replace `my-repo` with your own repository. Note also that AWS CodeCommit has different URLs depending the region in which you are working.
-
-:::{note}
-The support for protocols other than HTTPS is not available at this time.
-:::
-
-## Private server configuration
-
-Nextflow is able to access repositories hosted on private BitBucket, GitHub, GitLab and Gitea server installations.
-
-In order to use a private SCM installation you will need to set the server name and access credentials in your [SCM configuration file](#scm-configuration-file) .
-
-If, for example, the host name of your private GitLab server is `gitlab.acme.org`, you will need to have in the `$HOME/.nextflow/scm` file a configuration like the following:
-
-```groovy
-providers {
-    mygit {
-        server = 'http://gitlab.acme.org'
-        platform = 'gitlab'
-        user = 'your-user'
-        password = 'your-password'
-        token = 'your-api-token'
-    }
-}
-```
-
-Then you will be able to run/pull a project with Nextflow using the following command line:
-
-```bash
-nextflow run foo/bar -hub mygit
-```
-
-Or, in alternative, using the Git clone URL:
-
-```bash
-nextflow run http://gitlab.acme.org/foo/bar.git
-```
-
-:::{note}
-You must also specify the server API endpoint URL if it differs from the server base URL. For example, for GitHub Enterprise V3, add `endpoint = 'https://git.your-domain.com/api/v3'`.
-:::
-
-:::{warning}
-When accessing a private SCM installation over `https` from a server that uses a custom SSL certificate, you may need to import the certificate into your local Java keystore. Read more [here](https://docs.oracle.com/javase/tutorial/security/toolsign/rstep2.html).
-:::
-
-## Local repository configuration
-
-Nextflow is also able to handle repositories stored in a local or shared file system. The repository must be created as a [bare repository](https://mijingo.com/blog/what-is-a-bare-git-repository).
-
-Having, for example. a bare repository store at path `/shared/projects/foo.git`, Nextflow is able to run it using the following syntax:
+For example, given a bare repository at `/shared/projects/foo.git`, Nextflow is able to run it using the following syntax:
 
 ```bash
 nextflow run file:/shared/projects/foo.git
@@ -426,119 +50,118 @@ or
 nextflow run http://github.com/foo/bar
 ```
 
-See the [Running a pipeline](#running-a-pipeline) section for more details on how to run Nextflow projects.
+See the {ref}`CLI <cli-page>` page to learn how to use the Nextflow command line to run pipelines and manage pipeline projects.
 
-## Manage dependencies
+## Managing dependencies
 
-Computational pipelines are rarely composed by a single script. In real world applications they depend on dozens of other components. These can be other scripts, databases, or applications compiled for a platform native binary format.
+Computational pipelines are rarely composed by a single script. In real world applications they depend on many other components, including other scripts and tools, databases, and specialized environments which provide compute and storage.
 
-External dependencies are the most common source of problems when sharing a piece of software, because the users need to have an identical set of tools and the same configuration to be able to use it. In many cases this has proven to be a painful and error prone process, that can severely limit the ability to reproduce computational results on a system other than the one on which it was originally developed.
+These external dependencies are the primary challenge when sharing software, because the users need to recreate the environment around a tool in order to use it. This setup process is often painful and error prone, which severely hinders the ability to reproduce computational results on a system other than the one on which it was originally developed.
 
-Nextflow tackles this problem by integrating GitHub, BitBucket and GitLab sharing platforms and [Docker](http://www.docker.com) containers technology.
+Nextflow tackles this problem by integrating with existing tools for reproducible software, namely Git for source code and Docker for containers. These tools allow you to keep all the dependencies of your pipeline project in one place and track changes over time with version control.
 
-The use of a code management system is important to keep together all the dependencies of your pipeline project and allows you to track the changes of the source code in a consistent manner.
+By making your pipeline project is self-contained, meaning all of its dependencies are fully defined in the project itself, you gain two major advantages:
 
-Moreover to guarantee that a pipeline is reproducible it should be self-contained i.e. it should have ideally no dependencies on the hosting environment. By using Nextflow you can achieve this goal following these methods:
+- **Portability**: the pipeline can be run in virtually any environment with a Java VM and a container runtime
+- **Reproducibility**: any results produced by the pipelined can be easily reproduced, even across different environments
 
-### Binary applications
+One way to account for dependencies is to break them down into three categories: code, data, and environment. Here we will describe how to include each of these dependencies in your Nextflow pipeline:
 
-Docker allows you to ship any binary dependencies that you may have in your pipeline to a portable image that is downloaded on-demand and can be executed on any platform where a Docker engine is installed.
+### Code
 
-In order to use it with Nextflow, create a Docker image containing the tools needed by your pipeline and make it available in the [Docker Hub](https://hub.docker.com).
+Aside from pipeline scripts, you may have additional scripts and tools used by individual tasks.
 
-Then declare in the `nextflow.config` file, that you will include in your project, the name of the Docker image you have created. For example:
+#### Standard dependencies
+
+Many standard tools can be accessed as Docker containers or Conda/Spack packages. In this case, you only need to specify the container image URL (e.g. from [DockerHub](https://hub.docker.com)) or package name with the `container` or `conda` directive, respectively.
+
+Make sure to enable the desired method in your Nextflow configuration:
 
 ```groovy
-process.container = 'my-docker-image'
+// containers
 docker.enabled = true
-```
 
-In this way when you launch the pipeline execution, the Docker image will be automatically downloaded and used to run your tasks.
+// conda packages
+conda.enabled = true
+```
 
-Read the {ref}`container-page` page to learn more on how to use containers with Nextflow.
+This way, when you launch your pipeline, Nextflow will automatically download the necessary dependencies to run your tasks based on this configuration.
 
-This mix of technologies makes it possible to write self-contained and truly reproducible pipelines which require zero configuration and can be reproduced in any system having a Java VM and a Docker engine installed.
+Read the {ref}`container-page` page to learn more about how to use containers with Nextflow, and the {ref}`conda-page` page for Conda packages.
 
-[^id2]: BitBucket provides two types of version control system: Git and Mercurial. Nextflow supports only Git repositories.
+:::{tip}
+For maximal reproducibility, make sure to define a specific version for each tool. Otherwise, your pipeline might use different versions across subsequent runs, which can introduce subtle differences to your results.
+:::
 
 (bundling-executables)=
 
-### Bundling executables in the workflow
-
-In most cases, software dependencies should be provided by the execution environment ([container](./container.md), [conda](./conda.md)/[spack](./spack.md) environment, or host-native [modules](./process.md#module)). 
+#### The `bin` directory
 
-In cases where you do not wish to modify the execution environment(s), executable scripts can be included in the `bin/` directory in the workflow repository root. This can be useful to make changes that affect task execution across all environments with a single change.
+As for custom scripts, you can include executable scripts in the `bin` directory of your pipeline repository. When configured correctly, these scripts can be executed like a regular command from any process script (i.e. without modifying the `PATH` environment variable or using an absolute path), and changing the script will cause the task to be re-executed on a resumed run (i.e. just like changing the process script itself).
 
-To ensure your scripts can be made available to the task:
+To configure a custom script:
 
-1. Write scripts in the `bin/` directory (relative to the project repository root)
+1. Save the script in the `bin` directory (relative to the pipeline repository root).
 2. Specify a portable shebang (see note below for details).
-3. Ensure the scripts are executable. For example: `chmod a+x bin/my_script.py`
+3. Make the script executable. For example: `chmod a+x bin/my_script.py`
 
 :::{tip}
-To maximize portability of your bundled script, it is recommended to avoid hard-coding the interpreter path in the shebang line. 
+To maximize the portability of your bundled script, use `env` to dynamically resolve the location of the interpreter instead of hard-coding it in the shebang line.
 
-For example, shebang definitions `#!/usr/bin/python` and `#!/usr/local/bin/python` both hard-code specific paths to the python interpreter. To improve portability, rely on `env` to dynamically resolve the path to the interpreter. An example of the recommended approach is:
+For example, shebang definitions `#!/usr/bin/python` and `#!/usr/local/bin/python` both hard-code specific paths to the Python interpreter. Instead, the following approach is more portable:
 
 ```bash
 #!/usr/bin/env python
 ```
 :::
 
-### Using bundled executables in the workflow 
-
-Nextflow will automatically add the `bin/` directory to the `PATH` environment variable, and the scripts will automatically be accessible in your pipeline without the need to specify an absolute path to invoke them.
-
-### Utility code
+#### The `lib` directory
 
 Any Groovy scripts or JAR files in the `lib` directory will be automatically loaded and made available to your pipeline scripts. The `lib` directory is a useful way to provide utility code or external libraries without cluttering the pipeline scripts.
 
-### System environment
+### Data
+
+In general, input data should be provided by external sources using parameters which can be controlled by the user. This way, a pipeline can be easily reused to process different datasets which are appropriate for the pipeline.
 
-Any environment variable that may be required by the tools in your pipeline can be defined in the `nextflow.config` file by using the `env` scope and including it in the root directory of your project. For example:
+Parameters can be declared with default values in the main script or in the configuration file:
 
 ```groovy
-env {
-  DELTA = 'foo'
-  GAMMA = 'bar'
-}
+params.my_input = 'default input file'
+params.my_output = 'default output path'
+params.my_flag = false
+// ...
 ```
 
-See the {ref}`config-page` page to learn more about the Nextflow configuration file.
-
-### Resource manager
-
-When using Nextflow you don't need to write the code to parallelize your pipeline for a specific grid engine/resource manager because the parallelization is defined implicitly and managed by the Nextflow runtime. The target execution environment is parametrized and defined in the configuration file, thus your code is free from this kind of dependency.
-
-### Bootstrap data
+When launching a pipeline, parameter values can be provided on the command line or in a params file (using the `-params-file` option). Options prefixed with a double dash (`--`) are interpreted as parameters:
 
-Whenever your pipeline requires some files or dataset to carry out any initialization step, you can include this data in the pipeline repository itself and distribute them together.
+```bash
+nextflow run <your pipeline> --my_input /path/to/input/file --my_output /other/path --my_flag true
+```
 
-To reference this data in your pipeline script in a portable manner (i.e. without the need to use a static absolute path) use the implicit variable `baseDir` which locates the base directory of your pipeline project.
+When a pipeline requires some small data that rarely changes, it may be easier to include the data in the pipeline repository. You can reference this data from the pipeline script in a portable manner (i.e. without relying on an absolute path) by using the `projectDir` implicit variable, which refers to the local copy of the pipeline repository.
 
-For example, you can create a folder named `dataset/` in your repository root directory and copy there the required data file(s) you may need, then you can access this data in your script by writing:
+The following example references the file `dataset/sequences.fa` in the pipeline repository:
 
-```groovy
-sequences = file("$baseDir/dataset/sequences.fa")
+```nextflow
+sequences = file("$projectDir/dataset/sequences.fa")
 sequences.splitFasta {
     println it
 }
 ```
 
-### User inputs
+### Environment
+
+The "environment" refers to any other aspects of the environment in which your pipeline is executed, such as environment variables and resource managers like SLURM.
 
-Nextflow scripts can be easily parametrised to allow users to provide their own input data. Simply declare on the top of your script all the parameters it may require as shown below:
+Any environment variable that may be required by the tools in your pipeline can be defined under the `env` scope in your Nextflow configuration. For example:
 
 ```groovy
-params.my_input = 'default input file'
-params.my_output = 'default output path'
-params.my_flag = false
-// ...
+env {
+  DELTA = 'foo'
+  GAMMA = 'bar'
+}
 ```
 
-The actual parameter values can be provided when launching the script execution on the command line by prefixed the parameter name with a double minus character i.e. `--`, for example:
-
-```bash
-nextflow run <your pipeline> --my_input /path/to/input/file --my_output /other/path --my_flag true
-```
+Similarly, if you use an HPC scheduler like SLURM or a cloud batch service like AWS Batch to execute tasks in a distributed manner, you can use a configuration profile to define the settings for a given environment.
 
+See {ref}`config-page` for more information about Nextflow configuration and {ref}`executor-page` for more information about executors.
diff --git a/docs/snippets/branch-criteria.nf b/docs/snippets/branch-criteria.nf
index 9730317433..741d3210b2 100644
--- a/docs/snippets/branch-criteria.nf
+++ b/docs/snippets/branch-criteria.nf
@@ -1,12 +1,12 @@
-def criteria = branchCriteria {
-    small: it < 10
-    large: it > 10
+def criteria = branchCriteria { v ->
+    small: v < 10
+    large: v > 10
 }
 
 Channel.of(1, 2, 30).branch(criteria).set { ch1 }
 Channel.of(10, 20, 3).branch(criteria).set { ch2 }
 
-ch1.small.view { "$it is small" }
-ch1.large.view { "$it is large" }
-ch2.small.view { "$it is small" }
-ch2.large.view { "$it is large" }
\ No newline at end of file
+ch1.small.view { v -> "$v is small" }
+ch1.large.view { v -> "$v is large" }
+ch2.small.view { v -> "$v is small" }
+ch2.large.view { v -> "$v is large" }
\ No newline at end of file
diff --git a/docs/snippets/branch-with-fallback.nf b/docs/snippets/branch-with-fallback.nf
index b9ed430843..4d4f8f3168 100644
--- a/docs/snippets/branch-with-fallback.nf
+++ b/docs/snippets/branch-with-fallback.nf
@@ -1,11 +1,11 @@
 Channel.of(1, 2, 3, 40, 50)
-    .branch {
-        small: it < 10
-        large: it < 50
+    .branch { v ->
+        small: v < 10
+        large: v < 50
         other: true
     }
     .set { result }
 
-result.small.view { "$it is small" }
-result.large.view { "$it is large" }
-result.other.view { "$it is other" }
\ No newline at end of file
+result.small.view { v -> "$v is small" }
+result.large.view { v -> "$v is large" }
+result.other.view { v -> "$v is other" }
\ No newline at end of file
diff --git a/docs/snippets/branch-with-mapper.nf b/docs/snippets/branch-with-mapper.nf
index b7e98adb1a..b22bb36009 100644
--- a/docs/snippets/branch-with-mapper.nf
+++ b/docs/snippets/branch-with-mapper.nf
@@ -1,16 +1,16 @@
 Channel.of(1, 2, 3, 40, 50)
-    .branch {
-        foo: it < 10
-            return it+2
+    .branch { v ->
+        foo: v < 10
+            return v + 2
 
-        bar: it < 50
-            return it-2
+        bar: v < 50
+            return v - 2
 
         other: true
             return 0
     }
     .set { result }
 
-result.foo.view { "$it is foo" }
-result.bar.view { "$it is bar" }
-result.other.view { "$it is other" }
\ No newline at end of file
+result.foo.view { v -> "$v is foo" }
+result.bar.view { v -> "$v is bar" }
+result.other.view { v -> "$v is other" }
\ No newline at end of file
diff --git a/docs/snippets/branch.nf b/docs/snippets/branch.nf
index 973fd46800..98a03d5df2 100644
--- a/docs/snippets/branch.nf
+++ b/docs/snippets/branch.nf
@@ -1,9 +1,9 @@
 Channel.of(1, 2, 3, 40, 50)
-    .branch {
-        small: it < 10
-        large: it > 10
+    .branch { v ->
+        small: v < 10
+        large: v > 10
     }
     .set { result }
 
-result.small.view { "$it is small" }
-result.large.view { "$it is large" }
\ No newline at end of file
+result.small.view { v -> "$v is small" }
+result.large.view { v -> "$v is large" }
\ No newline at end of file
diff --git a/docs/snippets/buffer-with-closing.nf b/docs/snippets/buffer-with-closing.nf
index 36739fecf8..ebe119ff59 100644
--- a/docs/snippets/buffer-with-closing.nf
+++ b/docs/snippets/buffer-with-closing.nf
@@ -1,3 +1,3 @@
 Channel.of( 1, 2, 3, 1, 2, 3 )
-    .buffer { it == 2 }
+    .buffer { v -> v == 2 }
     .view()
\ No newline at end of file
diff --git a/docs/snippets/collect-with-mapper.nf b/docs/snippets/collect-with-mapper.nf
index ba9eda1ab3..b8908a7984 100644
--- a/docs/snippets/collect-with-mapper.nf
+++ b/docs/snippets/collect-with-mapper.nf
@@ -1,3 +1,3 @@
 Channel.of( 'hello', 'ciao', 'bonjour' )
-    .collect { it.length() }
+    .collect { v -> v.length() }
     .view()
\ No newline at end of file
diff --git a/docs/snippets/collectfile-closure.nf b/docs/snippets/collectfile-closure.nf
index c31e4e45f6..eeb949ec31 100644
--- a/docs/snippets/collectfile-closure.nf
+++ b/docs/snippets/collectfile-closure.nf
@@ -2,7 +2,7 @@ Channel.of('Hola', 'Ciao', 'Hello', 'Bonjour', 'Halo')
     .collectFile { item ->
         [ "${item[0]}.txt", item + '\n' ]
     }
-    .subscribe {
-        println "File '${it.name}' contains:"
-        println it.text
+    .subscribe { file ->
+        println "File '${file.name}' contains:"
+        println file.text
     }
\ No newline at end of file
diff --git a/docs/snippets/collectfile.nf b/docs/snippets/collectfile.nf
index c2295baa4c..ce931c87b3 100644
--- a/docs/snippets/collectfile.nf
+++ b/docs/snippets/collectfile.nf
@@ -1,6 +1,6 @@
 Channel.of('alpha', 'beta', 'gamma')
     .collectFile(name: 'sample.txt', newLine: true)
-    .subscribe {
-        println "Entries are saved to file: $it"
-        println "File content is: ${it.text}"
+    .subscribe { file ->
+        println "Entries are saved to file: $file"
+        println "File content is: ${file.text}"
     }
\ No newline at end of file
diff --git a/docs/snippets/count-with-filter-closure.nf b/docs/snippets/count-with-filter-closure.nf
index 7282cce013..afed9721eb 100644
--- a/docs/snippets/count-with-filter-closure.nf
+++ b/docs/snippets/count-with-filter-closure.nf
@@ -1,3 +1,3 @@
 Channel.of('a', 'c', 'c', 'q', 'b')
-    .count { it <= 'c' }
+    .count { v -> v <= 'c' }
     .view()
\ No newline at end of file
diff --git a/docs/snippets/cross-with-mapper.nf b/docs/snippets/cross-with-mapper.nf
index 7e20c3d6cc..4234e9cd06 100644
--- a/docs/snippets/cross-with-mapper.nf
+++ b/docs/snippets/cross-with-mapper.nf
@@ -1,4 +1,4 @@
 source = Channel.of( [1, 'alpha'], [2, 'beta'] )
 target = Channel.of( [1, 'a'], [1, 'b'], [2, 'a'], [2, 'b'] )
 
-source .cross(target) { it[1][0] } .view()
\ No newline at end of file
+source .cross(target) { v -> v[1][0] } .view()
\ No newline at end of file
diff --git a/docs/snippets/distinct-with-mapper.nf b/docs/snippets/distinct-with-mapper.nf
index b35422e4ee..386ee152ca 100644
--- a/docs/snippets/distinct-with-mapper.nf
+++ b/docs/snippets/distinct-with-mapper.nf
@@ -1,3 +1,3 @@
 Channel.of( 1, 1, 2, 2, 2, 3, 1, 1, 2, 4, 6 )
-    .distinct { it % 2 }
+    .distinct { v -> v % 2 }
     .view()
\ No newline at end of file
diff --git a/docs/snippets/dump.nf b/docs/snippets/dump.nf
index 7f3b482698..d2ae0686c6 100644
--- a/docs/snippets/dump.nf
+++ b/docs/snippets/dump.nf
@@ -1,7 +1,7 @@
 Channel.of( 1, 2, 3 )
-    .map { it+1 }
+    .map { v -> v + 1 }
     .dump(tag: 'foo')
 
 Channel.of( 1, 2, 3 )
-    .map { it^2 }
+    .map { v -> v ^ 2 }
     .dump(tag: 'bar')
\ No newline at end of file
diff --git a/docs/snippets/filter-closure.nf b/docs/snippets/filter-closure.nf
index 59578268e7..43fbfd6454 100644
--- a/docs/snippets/filter-closure.nf
+++ b/docs/snippets/filter-closure.nf
@@ -1,3 +1,3 @@
 Channel.of( 1, 2, 3, 4, 5 )
-    .filter { it % 2 == 1 }
+    .filter { v -> v % 2 == 1 }
     .view()
\ No newline at end of file
diff --git a/docs/snippets/first.nf b/docs/snippets/first.nf
index d4ec5d15df..740c8fc132 100644
--- a/docs/snippets/first.nf
+++ b/docs/snippets/first.nf
@@ -15,5 +15,5 @@ Channel.of( 1, 2, 'a', 'b', 3 )
 
 // emits the first item for which the predicate evaluates to true: 4
 Channel.of( 1, 2, 3, 4, 5 )
-    .first { it > 3 }
+    .first { v -> v > 3 }
     .view()
\ No newline at end of file
diff --git a/docs/snippets/flatmap-map.nf b/docs/snippets/flatmap-map.nf
index fd78c38674..2bb3f01ab0 100644
--- a/docs/snippets/flatmap-map.nf
+++ b/docs/snippets/flatmap-map.nf
@@ -1,3 +1,3 @@
 Channel.of( 1, 2, 3 )
     .flatMap { n -> [ number: n, square: n*n, cube: n*n*n ] }
-    .view { "${it.key}: ${it.value}" }
\ No newline at end of file
+    .view { entry -> "${entry.key}: ${entry.value}" }
\ No newline at end of file
diff --git a/docs/snippets/grouptuple-groupkey.nf b/docs/snippets/grouptuple-groupkey.nf
index fa9f08c6fd..5c8fce8e7a 100644
--- a/docs/snippets/grouptuple-groupkey.nf
+++ b/docs/snippets/grouptuple-groupkey.nf
@@ -1,12 +1,13 @@
-chr_frequency = ["chr1": 2, "chr2": 3]
-
 Channel.of(
-        ['region1', 'chr1', '/path/to/region1_chr1.vcf'],
-        ['region2', 'chr1', '/path/to/region2_chr1.vcf'],
-        ['region1', 'chr2', '/path/to/region1_chr2.vcf'],
-        ['region2', 'chr2', '/path/to/region2_chr2.vcf'],
-        ['region3', 'chr2', '/path/to/region3_chr2.vcf']
+        ['chr1', ['/path/to/region1_chr1.vcf', '/path/to/region2_chr1.vcf']],
+        ['chr2', ['/path/to/region1_chr2.vcf', '/path/to/region2_chr2.vcf', '/path/to/region3_chr2.vcf']],
     )
-    .map { region, chr, vcf -> tuple( groupKey(chr, chr_frequency[chr]), vcf ) }
+    .flatMap { chr, vcfs ->
+        vcfs.collect { vcf ->
+            tuple(groupKey(chr, vcfs.size()), vcf)              // preserve group size with key
+        }
+    }
+    .view { v -> "scattered: ${v}" }
     .groupTuple()
-    .view()
\ No newline at end of file
+    .map { key, vcfs -> tuple(key.getGroupTarget(), vcfs) }     // unwrap group key
+    .view { v -> "gathered: ${v}" }
\ No newline at end of file
diff --git a/docs/snippets/grouptuple-groupkey.out b/docs/snippets/grouptuple-groupkey.out
index e97159c872..be3f00185b 100644
--- a/docs/snippets/grouptuple-groupkey.out
+++ b/docs/snippets/grouptuple-groupkey.out
@@ -1,2 +1,7 @@
-[chr1, [/path/to/region1_chr1.vcf, /path/to/region2_chr1.vcf]]
-[chr2, [/path/to/region1_chr2.vcf, /path/to/region2_chr2.vcf, /path/to/region3_chr2.vcf]]
\ No newline at end of file
+scattered: [chr1, /path/to/region1_chr1.vcf]
+scattered: [chr1, /path/to/region2_chr1.vcf]
+scattered: [chr2, /path/to/region1_chr2.vcf]
+scattered: [chr2, /path/to/region2_chr2.vcf]
+scattered: [chr2, /path/to/region3_chr2.vcf]
+gathered: [chr1, [/path/to/region1_chr1.vcf, /path/to/region2_chr1.vcf]]
+gathered: [chr2, [/path/to/region1_chr2.vcf, /path/to/region2_chr2.vcf, /path/to/region3_chr2.vcf]]
\ No newline at end of file
diff --git a/docs/snippets/map.nf b/docs/snippets/map.nf
index a4df86f706..3a6b302f7b 100644
--- a/docs/snippets/map.nf
+++ b/docs/snippets/map.nf
@@ -1,3 +1,3 @@
 Channel.of( 1, 2, 3, 4, 5 )
-    .map { it * it }
+    .map { v -> v * v }
     .view()
\ No newline at end of file
diff --git a/docs/snippets/max-with-comparator.nf b/docs/snippets/max-with-comparator.nf
index 9be747b11c..26bb2df174 100644
--- a/docs/snippets/max-with-comparator.nf
+++ b/docs/snippets/max-with-comparator.nf
@@ -1,4 +1,4 @@
 // comparator function
 Channel.of( "hello", "hi", "hey" )
-    .max { a, b -> a.size() <=> b.size() }
+    .max { a, b -> a.length() <=> b.length() }
     .view()
\ No newline at end of file
diff --git a/docs/snippets/max-with-mapper.nf b/docs/snippets/max-with-mapper.nf
index e047f1a4ea..c428a022e3 100644
--- a/docs/snippets/max-with-mapper.nf
+++ b/docs/snippets/max-with-mapper.nf
@@ -1,4 +1,4 @@
 // mapping function
 Channel.of( "hello", "hi", "hey" )
-    .max { it.size() }
+    .max { v -> v.length() }
     .view()
\ No newline at end of file
diff --git a/docs/snippets/max.nf b/docs/snippets/max.nf
index d2b321416a..79e221b6cf 100644
--- a/docs/snippets/max.nf
+++ b/docs/snippets/max.nf
@@ -1,3 +1,3 @@
 Channel.of( 8, 6, 2, 5 )
     .max()
-    .view { "Max value is $it" }
\ No newline at end of file
+    .view { v -> "Max value is $v" }
\ No newline at end of file
diff --git a/docs/snippets/min-with-comparator.nf b/docs/snippets/min-with-comparator.nf
index 3392c95a0e..85fe62a26e 100644
--- a/docs/snippets/min-with-comparator.nf
+++ b/docs/snippets/min-with-comparator.nf
@@ -1,4 +1,4 @@
 // comparator function
 Channel.of( "hello", "hi", "hey" )
-    .min { a, b -> a.size() <=> b.size() }
+    .min { a, b -> a.length() <=> b.length() }
     .view()
\ No newline at end of file
diff --git a/docs/snippets/min-with-mapper.nf b/docs/snippets/min-with-mapper.nf
index 32ab5287f3..957d993426 100644
--- a/docs/snippets/min-with-mapper.nf
+++ b/docs/snippets/min-with-mapper.nf
@@ -1,4 +1,4 @@
 // mapping function
 Channel.of( "hello", "hi", "hey" )
-    .min { it.size() }
+    .min { v -> v.length() }
     .view()
\ No newline at end of file
diff --git a/docs/snippets/min.nf b/docs/snippets/min.nf
index 78ab2571fe..9cedee3a05 100644
--- a/docs/snippets/min.nf
+++ b/docs/snippets/min.nf
@@ -1,3 +1,3 @@
 Channel.of( 8, 6, 2, 5 )
     .min()
-    .view { "Min value is $it" }
\ No newline at end of file
+    .view { v -> "Min value is $v" }
\ No newline at end of file
diff --git a/docs/snippets/multimap-criteria.nf b/docs/snippets/multimap-criteria.nf
index 7b15740d97..4a00af187d 100644
--- a/docs/snippets/multimap-criteria.nf
+++ b/docs/snippets/multimap-criteria.nf
@@ -1,6 +1,6 @@
-def criteria = multiMapCriteria {
-    small: [it, it < 10]
-    large: [it, it > 10]
+def criteria = multiMapCriteria { v ->
+    small: [v, v < 10]
+    large: [v, v > 10]
 }
 
 Channel.of(1, 2, 30).multiMap(criteria).set { ch1 }
diff --git a/docs/snippets/multimap-shared.nf b/docs/snippets/multimap-shared.nf
index 0573f53199..8d8831cbae 100644
--- a/docs/snippets/multimap-shared.nf
+++ b/docs/snippets/multimap-shared.nf
@@ -1,6 +1,6 @@
 Channel.of( 1, 2, 3 )
-    .multiMap { it -> foo: bar: it }
+    .multiMap { v -> foo: bar: v }
     .set { result }
 
-result.foo.view { "foo $it" }
-result.bar.view { "bar $it" }
\ No newline at end of file
+result.foo.view { v -> "foo $v" }
+result.bar.view { v -> "bar $v" }
\ No newline at end of file
diff --git a/docs/snippets/multimap.nf b/docs/snippets/multimap.nf
index 52ab934aca..67ce2a9ab5 100644
--- a/docs/snippets/multimap.nf
+++ b/docs/snippets/multimap.nf
@@ -1,9 +1,9 @@
 Channel.of( 1, 2, 3, 4 )
-    .multiMap { it ->
-        foo: it + 1
-        bar: it * it
+    .multiMap { v ->
+        foo: v + 1
+        bar: v * v
     }
     .set { result }
 
-result.foo.view { "foo $it" }
-result.bar.view { "bar $it" }
\ No newline at end of file
+result.foo.view { v -> "foo $v" }
+result.bar.view { v -> "bar $v" }
\ No newline at end of file
diff --git a/docs/snippets/process-out-env.nf b/docs/snippets/process-out-env.nf
index 848d2f9f82..8ac03a1880 100644
--- a/docs/snippets/process-out-env.nf
+++ b/docs/snippets/process-out-env.nf
@@ -1,6 +1,6 @@
 process myTask {
     output:
-    env FOO
+    env 'FOO'
 
     script:
     '''
diff --git a/docs/snippets/process-stdout.nf b/docs/snippets/process-stdout.nf
index 9e2e719896..803957c778 100644
--- a/docs/snippets/process-stdout.nf
+++ b/docs/snippets/process-stdout.nf
@@ -8,5 +8,5 @@ process sayHello {
 }
 
 workflow {
-    sayHello | view { "I say... $it" }
+    sayHello | view { message -> "I say... $message" }
 }
\ No newline at end of file
diff --git a/docs/snippets/reduce-with-initial-value.nf b/docs/snippets/reduce-with-initial-value.nf
index 28427b32a8..afe25d7b2f 100644
--- a/docs/snippets/reduce-with-initial-value.nf
+++ b/docs/snippets/reduce-with-initial-value.nf
@@ -1,6 +1,6 @@
 Channel.of( 1, 2, 3, 4, 5 )
-    .reduce( 'result:' ) { accum, v ->
-        println accum
-        accum + ' ' + v
+    .reduce( 'result:' ) { acc, v ->
+        println acc
+        acc + ' ' + v
     }
-    .view { "final $it" }
\ No newline at end of file
+    .view { result -> "final $result" }
\ No newline at end of file
diff --git a/docs/snippets/reduce.nf b/docs/snippets/reduce.nf
index f4c0402269..34206f7562 100644
--- a/docs/snippets/reduce.nf
+++ b/docs/snippets/reduce.nf
@@ -3,4 +3,4 @@ Channel.of( 1, 2, 3, 4, 5 )
         println "a: $a b: $b"
         a + b
     }
-    .view { "result = $it" }
\ No newline at end of file
+    .view { result -> "result = $result" }
\ No newline at end of file
diff --git a/docs/snippets/splitjson-array.nf b/docs/snippets/splitjson-array.nf
index 99b81ab1b8..b3b76b15a0 100644
--- a/docs/snippets/splitjson-array.nf
+++ b/docs/snippets/splitjson-array.nf
@@ -1,4 +1,4 @@
 // Example with a JSON array
 Channel.of('[1, null, ["A", {}], true]')
     .splitJson()
-    .view{"Item: ${it}"}
\ No newline at end of file
+    .view { v -> "Item: ${v}" }
\ No newline at end of file
diff --git a/docs/snippets/splitjson-object.nf b/docs/snippets/splitjson-object.nf
index 8f403576f6..7958d4030c 100644
--- a/docs/snippets/splitjson-object.nf
+++ b/docs/snippets/splitjson-object.nf
@@ -1,4 +1,4 @@
 // Example with a JSON object
 Channel.of('{"A": 1, "B": [1, 2, 3], "C": {"D": null}}')
     .splitJson()
-    .view{"Item: ${it}"}
\ No newline at end of file
+    .view { v -> "Item: ${v}" }
\ No newline at end of file
diff --git a/docs/snippets/splitjson-with-path.nf b/docs/snippets/splitjson-with-path.nf
index 15a652d53b..883eca07fc 100644
--- a/docs/snippets/splitjson-with-path.nf
+++ b/docs/snippets/splitjson-with-path.nf
@@ -1,3 +1,3 @@
 Channel.of('{"A": 1, "B": [2, 3, {"C": {"D": null, "E": 4, "F": 5}}]}')
     .splitJson(path: 'B[2].C')
-    .view{"Item: ${it}"}
\ No newline at end of file
+    .view { v -> "Item: ${v}" }
\ No newline at end of file
diff --git a/docs/snippets/subscribe-with-on-complete.nf b/docs/snippets/subscribe-with-on-complete.nf
index fa44724378..4f2b73fb03 100644
--- a/docs/snippets/subscribe-with-on-complete.nf
+++ b/docs/snippets/subscribe-with-on-complete.nf
@@ -1,2 +1,2 @@
 Channel.of( 1, 2, 3 )
-    .subscribe onNext: { println it }, onComplete: { println 'Done' }
\ No newline at end of file
+    .subscribe onNext: { v -> println v }, onComplete: { println 'Done' }
\ No newline at end of file
diff --git a/docs/snippets/subscribe-with-param.nf b/docs/snippets/subscribe-with-param.nf
deleted file mode 100644
index 273e519ce3..0000000000
--- a/docs/snippets/subscribe-with-param.nf
+++ /dev/null
@@ -1,5 +0,0 @@
-Channel
-    .of( 'alpha', 'beta', 'lambda' )
-    .subscribe { String str ->
-        println "Got: ${str}; len: ${str.size()}"
-    }
\ No newline at end of file
diff --git a/docs/snippets/subscribe-with-param.out b/docs/snippets/subscribe-with-param.out
deleted file mode 100644
index 3be852e6b9..0000000000
--- a/docs/snippets/subscribe-with-param.out
+++ /dev/null
@@ -1,3 +0,0 @@
-Got: alpha; len: 5
-Got: beta; len: 4
-Got: lambda; len: 6
\ No newline at end of file
diff --git a/docs/snippets/subscribe.nf b/docs/snippets/subscribe.nf
index e5a4a3b8f0..f17b933132 100644
--- a/docs/snippets/subscribe.nf
+++ b/docs/snippets/subscribe.nf
@@ -2,4 +2,4 @@
 source = Channel.of( 'alpha', 'beta', 'delta' )
 
 // subscribe to the channel with a function that prints each value
-source.subscribe { println "Got: $it" }
\ No newline at end of file
+source.subscribe { str -> println "Got: ${str}; len: ${str.length()}" }
\ No newline at end of file
diff --git a/docs/snippets/subscribe.out b/docs/snippets/subscribe.out
index 27a68821f4..47e4bfcb14 100644
--- a/docs/snippets/subscribe.out
+++ b/docs/snippets/subscribe.out
@@ -1,3 +1,3 @@
-Got: alpha
-Got: beta
-Got: delta
\ No newline at end of file
+Got: alpha; len: 5
+Got: beta; len: 4
+Got: delta; len: 5
diff --git a/docs/snippets/sum-with-mapper.nf b/docs/snippets/sum-with-mapper.nf
index 9824e9bade..21c34fe47e 100644
--- a/docs/snippets/sum-with-mapper.nf
+++ b/docs/snippets/sum-with-mapper.nf
@@ -1,3 +1,3 @@
 Channel.of( 4, 1, 7, 5 )
-    .sum { it * it }
-    .view { "Square: $it" }
\ No newline at end of file
+    .sum { v -> v * v }
+    .view { result -> "Square: $result" }
\ No newline at end of file
diff --git a/docs/snippets/sum.nf b/docs/snippets/sum.nf
index add3d63e1f..adc740fc22 100644
--- a/docs/snippets/sum.nf
+++ b/docs/snippets/sum.nf
@@ -1,3 +1,3 @@
 Channel.of( 8, 6, 2, 5 )
     .sum()
-    .view { "The sum is $it" }
\ No newline at end of file
+    .view { result -> "The sum is $result" }
\ No newline at end of file
diff --git a/docs/snippets/tap.nf b/docs/snippets/tap.nf
index 41278f9711..d244d7f141 100644
--- a/docs/snippets/tap.nf
+++ b/docs/snippets/tap.nf
@@ -1,9 +1,9 @@
 Channel.of( 'a', 'b', 'c' )
     .tap { log1 }
-    .map { it * 2 }
+    .map { v -> v * 2 }
     .tap { log2 }
-    .map { it.toUpperCase() }
-    .view { "Result: $it" }
+    .map { v -> v.toUpperCase() }
+    .view { result -> "Result: $result" }
 
-log1.view { "Log 1: $it" }
-log2.view { "Log 2: $it" }
\ No newline at end of file
+log1.view { v -> "Log 1: $v" }
+log2.view { v -> "Log 2: $v" }
\ No newline at end of file
diff --git a/docs/snippets/unique-with-mapper.nf b/docs/snippets/unique-with-mapper.nf
index 3eee3005f0..c2ba1b4640 100644
--- a/docs/snippets/unique-with-mapper.nf
+++ b/docs/snippets/unique-with-mapper.nf
@@ -1,3 +1,3 @@
 Channel.of( 1, 1, 2, 2, 2, 3, 1, 1, 2, 4, 6 )
-    .unique { it % 2 }
+    .unique { v -> v % 2 }
     .view()
\ No newline at end of file
diff --git a/docs/snippets/until.nf b/docs/snippets/until.nf
index 9fe22e26fa..528b2aa136 100644
--- a/docs/snippets/until.nf
+++ b/docs/snippets/until.nf
@@ -1,3 +1,3 @@
 Channel.of( 3, 2, 1, 5, 1, 5 )
-    .until { it == 5 }
+    .until { v -> v == 5 }
     .view()
\ No newline at end of file
diff --git a/docs/snippets/view-with-mapper.nf b/docs/snippets/view-with-mapper.nf
index 643cfd4394..60344c4de3 100644
--- a/docs/snippets/view-with-mapper.nf
+++ b/docs/snippets/view-with-mapper.nf
@@ -1,3 +1,3 @@
 Channel.of(1, 2, 3)
-    .map { it -> [it, it*it] }
+    .map { v -> [v, v*v] }
     .view { num, sqr -> "The square of $num is $sqr" }
\ No newline at end of file
diff --git a/docs/snippets/your-first-script.nf b/docs/snippets/your-first-script.nf
index 6fe3710e9b..0217cae8fc 100644
--- a/docs/snippets/your-first-script.nf
+++ b/docs/snippets/your-first-script.nf
@@ -22,5 +22,5 @@ process convertToUpper {
 }
 
 workflow {
-    splitLetters | flatten | convertToUpper | view { it.trim() }
+    splitLetters | flatten | convertToUpper | view { v -> v.trim() }
 }
diff --git a/docs/spack.md b/docs/spack.md
index 636b0952f8..922947beb0 100644
--- a/docs/spack.md
+++ b/docs/spack.md
@@ -45,10 +45,11 @@ Alternatively, it can be specified by setting the variable `NXF_SPACK_ENABLED=tr
 
 Spack package names can specified using the `spack` directive. Multiple package names can be specified by separating them with a blank space. For example:
 
-```groovy
+```nextflow
 process foo {
   spack 'bwa samtools py-multiqc'
 
+  script:
   '''
   your_command --here
   '''
@@ -89,10 +90,11 @@ Read the Spack documentation for more details about how to create [environment f
 
 The path of an environment file can be specified using the `spack` directive:
 
-```groovy
+```nextflow
 process foo {
   spack '/some/path/my-env.yaml'
 
+  script:
   '''
   your_command --here
   '''
@@ -107,10 +109,11 @@ The environment file name **must** have a `.yaml` extension or else it won't be
 
 If you already have a local Spack environment, you can use it in your workflow specifying the installation directory of such environment by using the `spack` directive:
 
-```groovy
+```nextflow
 process foo {
   spack '/path/to/an/existing/env/directory'
 
+  script:
   '''
   your_command --here
   '''
diff --git a/docs/vscode.md b/docs/vscode.md
new file mode 100644
index 0000000000..11c847ae29
--- /dev/null
+++ b/docs/vscode.md
@@ -0,0 +1,569 @@
+(vscode-page)=
+
+# VS Code integration
+
+The [Nextflow VS Code extension](https://marketplace.visualstudio.com/items?itemName=nextflow.nextflow) provides IDE support for Nextflow pipelines.
+
+## Features
+
+### Syntax highlighting
+
+The VS Code extension highlights Nextflow scripts and config files for better readability.
+
+### Diagnostics
+
+The extension highlights source code in red for errors and yellow for warnings.
+
+To view all diagnostics for the workspace, open the **Problems** tab. Here, you can search for diagnostics by diagnostic message, filename, and so on.
+
+### Hover hints
+
+When you hover over certain source code elements, such as variable names and function calls, the extension provides a tooltip with related information, such as the definition and/or documentation for the element.
+
+### Code navigation
+
+The **Outline** section in the Explorer panel lists top-level definitions when you view a script. Include declarations in scripts and config files act as links, and ctrl-clicking them opens the corresponding script or config file.
+
+To view the definition of a symbol (e.g., a workflow, process, function, or variable), right-click the symbol and select **Go to Definition**. Ctrl-click the symbol to view the definition. Ctrl-click the definition to show all references.
+
+### Code completion
+
+The extension suggests auto-completions for variable names, function names, config settings, and other symbols as you type. The extension also provides several snippets for common script declarations, such as processes and workflows.
+
+### Formatting
+
+The extension can format your scripts and config files based on a standard set of formatting rules. Rules can be customized using the **Nextflow > Formatting** [extension settings](#settings).
+
+Use the **Format Document** command in the command palette to format the current file.
+
+### Renaming symbols
+
+The extension can rename all references of a symbol (e.g., a workflow, process, function, or variable) throughout the code.
+
+To rename a symbol, right-click the symbol, select **Rename Symbol**, and enter a new name.
+
+### Parameter schema
+
+If a `nextflow_schema.json` file exists in the same directory as a script with an entry workflow, the extension uses the schema to provide validation, hover hints, and code completion for params in the entry workflow.
+
+### DAG preview for workflows
+
+The extension can generate a workflow DAG that includes the workflow inputs, outputs, and any processes or workflows that are called by the selected workflow. The workflow DAG is displayed in a new panel to the side.
+
+To preview the DAG of a workflow, select the **Preview DAG** CodeLens above the workflow definition.
+
+:::{note}
+The **Preview DAG** CodeLens is only available when the script does not contain any errors.
+:::
+
+## Syntax guide
+
+The language server parses scripts and config files according to the {ref}`Nextflow language specification <syntax-page>`. It enforces a stricter syntax compared to the Nextflow CLI. As a result, the language server is able to perform more extensive error checking and provide more specific error messages. However, unlike the Nextflow CLI which allows all Groovy syntax, the Nextflow language specification is not a superset of Groovy. You may need to adjust your code to adhere to the strict syntax, especially if you use more advanced Groovy syntax.
+
+This section describes some of the most common unsupported features and how to address them. For a full description of the strict syntax, refer to the Nextflow language specification.
+
+:::{note}
+The "Nextflow language specification" is a strict specification of DSL2, not a new DSL version. The Nextflow language will be defined by this specification moving forward, rather than new DSL versions.
+:::
+
+:::{note}
+You can move unsupported code into the `lib` directory or a plugin, both of which support the full Groovy language.
+:::
+
+### Excluded syntax
+
+**Import declarations**
+
+In Groovy, the `import` declaration can be used to import external classes:
+
+```groovy
+import groovy.json.JsonSlurper
+
+def json = new JsonSlurper().parseText(json_file.text)
+```
+
+Instead, use the fully qualified name directly:
+
+```nextflow
+def json = new groovy.json.JsonSlurper().parseText(json_file.text)
+```
+
+**Class declarations**
+
+Some users use custom classes in Nextflow to define helper functions or custom record types. Instead, helper functions can be defined as standalone functions in a script. Custom record classes must be moved to the `lib` directory.
+
+:::{note}
+Record types will be addressed in a future version of the Nextflow language specification.
+:::
+
+:::{note}
+Enums, a special type of class, are supported, but cannot be included across modules at this time.
+:::
+
+**Mixing script declarations and statements**
+
+A script may contain any of the following top-level declarations:
+
+- Feature flags
+- Includes
+- Parameter declarations
+- Workflows
+- Processes
+- Functions
+- Output block
+
+Alternatively, a script may contain only statements, also known as a "code snippet":
+
+```nextflow
+println 'Hello world!'
+```
+
+Code snippets are treated as an implicit entry workflow:
+
+```nextflow
+workflow {
+    println 'Hello world!'
+}
+```
+
+Script declarations and statements cannot be mixed at the same level. All statements must reside within script declarations unless the script is a code snippet:
+
+```nextflow
+process foo {
+    // ...
+}
+
+// incorrect -- move into entry workflow
+// println 'Hello world!'
+
+// correct
+workflow {
+    println 'Hello world!'
+}
+```
+
+:::{note}
+Mixing statements and script declarations was necessary in DSL1 and allowed in DSL2. However, it is no longer supported in the Nextflow language specification in order to simplify the language and to ensure that top-level statements are only executed when the script is executed directly and not when it is included as a module.
+:::
+
+**Assignment expressions**
+
+In Groovy, you can assign a variable as part of an expression:
+
+```groovy
+foo(x = 1, y = 2)
+```
+
+The Nextflow language specification only allows assignment as statements:
+
+```nextflow
+x = 1
+y = 2
+foo(x, y)
+```
+
+The increment (`++`) and decrement (`--`) operators are no longer supported. Use `+=` and `-=` instead:
+
+```nextflow
+x += 1 // x++
+x -= 1 // x--
+```
+
+**For and while loops**
+
+Groovy supports loop statements such as `for` and `while`:
+
+```groovy
+for (rseqc_module in ['read_distribution', 'inner_distance', 'tin']) {
+    if (rseqc_modules.contains(rseqc_module))
+        rseqc_modules.remove(rseqc_module)
+}
+```
+
+The Nextflow language specification does not support loop statements. Use higher-order functions like the `each` method instead:
+
+```nextflow
+['read_distribution', 'inner_distance', 'tin'].each { rseqc_module ->
+    if (rseqc_modules.contains(rseqc_module))
+        rseqc_modules.remove(rseqc_module)
+}
+```
+
+Lists, maps, and sets provide several functions (e.g., `collect`, `find`, `findAll`, `inject`) for iteration. See [Groovy standard library](https://docs.groovy-lang.org/latest/html/groovy-jdk/overview-summary.html) for more information.
+
+**Switch statements**
+
+Groovy supports switch statements for pattern matching on a value:
+
+```groovy
+switch (aligner) {
+case 'bowtie2':
+    // ...
+    break
+case 'bwamem':
+    // ...
+    break
+case 'dragmap':
+    // ...
+    break
+case 'snap':
+    // ...
+    break
+default:
+    // ...
+}
+```
+
+The Nextflow language specification does not support switch statements. Use if-else statements instead:
+
+```nextflow
+if (aligner == 'bowtie2') {
+    // ...
+} else if (aligner == 'bwamem') {
+    // ...
+} else if (aligner == 'dragmap') {
+    // ...
+} else if (aligner == 'snap') {
+    // ...
+} else {
+    // ...
+}
+```
+
+**Implicit environment variables**
+
+In Nextflow DSL1 and DSL2, you can reference environment variables directly in strings:
+
+```nextflow
+println "PWD = ${PWD}"
+```
+
+The Nextflow language specification does not support implicit environment variables. Use `System.getenv()` instead:
+
+```nextflow
+println "PWD = ${System.getenv('PWD')}"
+```
+
+:::{versionadded} 24.11.0-edge
+The `env()` function can be used instead of `System.getenv()`:
+
+```nextflow
+println "PWD = ${env('PWD')}"
+```
+:::
+
+### Restricted syntax
+
+The following patterns are still supported but have been restricted, i.e. some syntax variants have been removed.
+
+**Variable declarations**
+
+In Groovy, variables can be declared in many different ways:
+
+```groovy
+def a = 1
+final b = 2
+def c = 3, d = 4
+def (e, f) = [5, 6]
+String str = 'foo'
+def Map meta = [:]
+```
+
+In Nextflow, variables should be declared with `def` and should not specify a type:
+
+```nextflow
+def a = 1
+def b = 2
+def (c, d) = [3, 4]
+def (e, f) = [5, 6]
+def str = 'foo'
+def meta = [:]
+```
+
+Similarly, functions should be declared with `def` and should not specify a return type or parameter types:
+
+```nextflow
+/**
+ * You can use comments to denote types, for example:
+ *
+ * @param x: Map
+ * @param y: String
+ * @param z: Integer
+ * @return List
+ */
+def foo(x, y, z) {
+    // ...
+}
+```
+
+To ease the migration of existing scripts, the language server only reports warnings for Groovy-style type annotations and implicit variable declarations. These warnings will become errors in the future.
+
+:::{note}
+Type annotations and static type checking will be addressed in a future version of the Nextflow language specification.
+:::
+
+**Strings**
+
+Groovy supports a wide variety of strings, including multi-line strings, dynamic strings, slashy strings, multi-line dynamic slashy strings, and more.
+
+The Nextflow language specification supports single- and double-quoted strings, multi-line strings, and slashy strings.
+
+Slashy strings cannot be interpolated:
+
+```nextflow
+def id = 'SRA001'
+assert 'SRA001.fastq' ~= /${id}\.f(?:ast)?q/
+```
+
+Use a double-quoted string instead:
+
+```nextflow
+def id = 'SRA001'
+assert 'SRA001.fastq' ~= "${id}\\.f(?:ast)?q"
+```
+
+Slashy strings cannot span multiple lines:
+
+```groovy
+/
+Patterns in the code,
+Symbols dance to match and find,
+Logic unconfined.
+/
+```
+
+Use a multi-line string instead:
+
+```nextflow
+"""
+Patterns in the code,
+Symbols dance to match and find,
+Logic unconfined.
+"""
+```
+
+Dollar slashy strings are not supported:
+
+```groovy
+$/
+echo "Hello world!"
+/$
+```
+
+Use a multi-line string instead:
+
+```nextflow
+"""
+echo "Hello world!"
+"""
+```
+
+**Process env inputs/outputs**
+
+In Nextflow DSL1 and DSL2, the name of a process `env` input/output can be specified with or without quotes:
+
+```nextflow
+process PROC {
+    input:
+    env FOO
+    env 'BAR'
+
+    // ...
+}
+```
+
+The Nextflow language specification requires the name to be specified with quotes:
+
+```nextflow
+process PROC {
+    input:
+    env 'FOO'
+    env 'BAR'
+
+    // ...
+}
+```
+
+**Implicit process script section**
+
+In Nextflow DSL1 and DSL2, the process `script:` section label can almost always be omitted:
+
+```nextflow
+process greet {
+    input:
+    val greeting
+
+    """
+    echo '${greeting}!'
+    """
+}
+```
+
+The Nextflow language specification allows the `script:` label to be omitted only if there are no other sections:
+
+```nextflow
+process sayHello {
+    """
+    echo 'Hello world!'
+    """
+}
+
+process greet {
+    input:
+    val greeting
+
+    script:
+    """
+    echo '${greeting}!'
+    """
+}
+```
+
+### Deprecated syntax
+
+The following patterns are deprecated. The language server reports "future warnings" for these patterns. Future warnings are disabled by default. Enable them by deselecting **Nextflow > Suppress Future Warnings** in the [extension settings](#settings). These warnings may become errors in the future.
+
+**Implicit closure parameter**
+
+In Groovy, a closure with no parameters is assumed to have a single parameter named `it`. The Nextflow language specification does not support implicit closure parameters. Declare the parameter explicitly instead:
+
+```nextflow
+ch | map { it * 2 }       // deprecated
+ch | map { v -> v * 2 }   // correct
+ch | map { it -> it * 2 } // also correct
+```
+
+**Using params outside the entry workflow**
+
+While params can be used anywhere in the pipeline code, they are only intended to be used in the entry workflow.
+
+Processes and workflows should receive params as explicit inputs:
+
+```nextflow
+process foo {
+    input:
+    val foo_args
+
+    // ...
+}
+
+workflow bar {
+    take:
+    bar_args
+
+    // ...
+}
+
+workflow {
+    foo(params.foo_args)
+    bar(params.bar_args)
+}
+```
+
+**Process each input**
+
+The `each` process input is deprecated. Use the `combine` or `cross` operator to explicitly repeat over inputs in the calling workflow.
+
+**Process when section**
+
+The process `when` section is deprecated. Use conditional logic, such as an `if` statement or the `filter` operator, to control the process invocation in the calling workflow.
+
+**Process shell section**
+
+The process `shell` section is deprecated. Use the `script` block instead. The VS Code extension provides syntax highlighting and error checking to help distinguish between Nextflow variables and Bash variables.
+
+### Configuration syntax
+
+See {ref}`config-syntax` for a comprehensive description of the configuration language.
+
+Currently, Nextflow parses config files as Groovy scripts, allowing the use of scripting constructs like variables, helper functions, and conditional logic for dynamic configuration. For example:
+
+```groovy
+def getHostname() {
+    // ...
+}
+
+def hostname = getHostname()
+if (hostname == 'small') {
+    params.max_memory = 32.GB
+    params.max_cpus = 8
+}
+else if (hostname == 'large') {
+    params.max_memory = 128.GB
+    params.max_cpus = 32
+}
+```
+
+The strict config syntax does not support functions, and only allows statements (e.g., variables and if statements) within closures. You can achieve the same dynamic configuration by using a dynamic include:
+
+```groovy
+includeConfig ({
+    def hostname = // ...
+    if (hostname == 'small')
+        return 'small.config'
+    else if (hostname == 'large')
+        return 'large.config'
+    else
+        return '/dev/null'
+}())
+```
+
+The include source is a closure that is immediately invoked. It includes a different config file based on the return value of the closure. Including `/dev/null` is equivalent to including nothing.
+
+Each conditional configuration is defined in a separate config file:
+
+```groovy
+// small.config
+params.max_memory = 32.GB
+params.max_cpus = 8
+
+// large.config
+params.max_memory = 128.GB
+params.max_cpus = 32
+```
+
+## Troubleshooting
+
+In the event of an error, you can stop or restart the language server from the command palette. See [Commands](#commands) for the set of available commands.
+
+Report issues at [nextflow-io/vscode-language-nextflow](https://github.com/nextflow-io/vscode-language-nextflow) or [nextflow-io/language-server](https://github.com/nextflow-io/language-server). When reporting, include a minimal code snippet that reproduces the issue and any error logs from the server. To view logs, open the **Output** tab and select **Nextflow Language Server** from the dropdown. Enable **Nextflow > Debug** in the [extension settings](#settings) to show additional log messages while debugging.
+
+## Limitations
+
+- The language server does not detect certain filesystem changes, such as changing the current Git branch. Restart the language server from the command palette to sync it with your workspace.
+
+- The language server does not recognize configuration options from third-party plugins and will report "Unrecognized config option" warnings for them.
+
+- The language server provides limited support for Groovy scripts in the `lib` directory. Errors in Groovy scripts are not reported as diagnostics, and changing a Groovy script does not automatically re-compile the Nextflow scripts that reference it. Edit the Nextflow script or close and re-open it to refresh the diagnostics.
+
+## Commands
+
+The following commands are available from the command palette:
+
+- Restart language server
+- Stop language server
+
+## Settings
+
+The following settings are available:
+
+`nextflow.debug`
+: Enable debug logging and debug information in hover hints.
+
+`nextflow.files.exclude`
+: Configure glob patterns for excluding folders from being searched for Nextflow scripts and configuration files.
+
+`nextflow.formatting.harshilAlignment`
+: Use the [Harshil Alignment™️](https://nf-co.re/docs/contributing/code_editors_and_styling/harshil_alignment) when formatting Nextflow scripts and config files.
+
+`nextflow.java.home`
+: Specifies the folder path to the JDK. Use this setting if the extension cannot find Java automatically.
+
+`nextflow.suppressFutureWarnings`
+: Hide warnings for future changes, deprecations, and removals.
+
+## Language server
+
+Most of the functionality of the VS Code extension is provided by the [Nextflow language server](https://github.com/nextflow-io/language-server), which implements the [Language Server Protocol (LSP)](https://microsoft.github.io/language-server-protocol/) for Nextflow scripts and config files.
+
+The language server is distributed as a standalone Java application. It can be integrated with any editor that functions as an LSP client. Currently, only the VS Code integration is officially supported, but community contributions for other editors are welcome.
diff --git a/docs/wave.md b/docs/wave.md
index 5b4d5a4d14..c27c034f6b 100644
--- a/docs/wave.md
+++ b/docs/wave.md
@@ -9,20 +9,6 @@
 
 ## Getting started
 
-### Nextflow installation
-
-If you have already installed Nextflow, update to the latest version using this command:
-
-```bash
-nextflow -self-update
-```
-
-If you don't have Nextflow already installed, install it with the command below:
-
-```bash
-curl get.nextflow.io | bash
-```
-
 ### Wave configuration
 
 Wave can be used in any Nextflow pipeline by adding the following snippet to your `nextflow.config` file:
@@ -104,33 +90,7 @@ conda.channels = 'conda-forge,bioconda'
 ```
 :::
 
-### Build Spack based containers
-
-:::{warning}
-Spack based Wave containers are currently in beta testing. Functionality is still sub-optimal, due to long build times that may result in backend time-out and subsequent task failure.
-:::
-
-Wave allows the provisioning of containers based on the {ref}`process-spack` directive used by the processes in your
-pipeline. This is an alternative to building Spack packages in the local computer.
-Moreover, this enables to run optimised builds with almost no user intervention.
-
-Having Wave enabled in your pipeline, there's nothing else to do other than define the `spack` requirements in
-the pipeline processes provided the same process does not also specify a `container` or `conda` directive or a Dockerfile.
-
-In the latter case, add the following setting to your pipeline configuration:
-
-```groovy
-wave.strategy = ['spack']
-```
-
-The above setting instructs Wave to only use the `spack` directive to provision the pipeline containers, ignoring the use of
-the `container` directive and any Dockerfile(s).
-
-In order to request the build of containers that are optimised for a specific CPU microarchitecture, the latter can be specified by means of the {ref}`process-arch` directive. The architecture must always be specified for processes that run on an ARM system. Otherwise, by default, Wave will build containers for the generic `x86_64` architecture family.
-
-:::{note}
-If using a Spack YAML file to provide the required packages, you should avoid editing the following sections, which are already configured by the Wave plugin: `packages`, `config`, `view` and `concretizer` (your edits may be ignored), and `compilers` (your edits will be considered, and may interfere with the setup by the Wave plugin).
-:::
+Packages from the [Python Package Index](https://pypi.org/) can also be added to a Conda `environment.yml` file. See {ref}`Conda and PyPI <conda-pypi>` for more information.
 
 (wave-singularity)=
 
@@ -187,6 +147,62 @@ The first repository is used to store the built container images. The second one
 The repository access keys must be provided as Seqera Platform credentials (see
 [Authenticate private repositories](#authenticate-private-repositories) above).
 
+### Mirroring containers
+
+Wave allows mirroring, i.e., copying containers used by your pipeline into a container registry of your choice. This allows the pipeline to pull containers from the target registry rather than the original registry.
+
+Mirroring is useful to create an on-demand cache of container images that are co-located in the same region where the pipeline
+is executed, and therefore optimising cost and network efficiency.
+
+Include the following settings in your Nextflow configuration to enable this capability:
+
+```groovy
+wave.enabled = true
+wave.mirror = true
+wave.build.repository = '<YOUR REGISTRY>'
+tower.accessToken = '<YOUR ACCESS TOKEN>'
+```
+
+In the above snippet, replace `<YOUR REGISTRY>` with a container registry of your choice. For example, `quay.io` (no prefix or suffix is needed).
+The container will be copied with the same name, tag, and checksum in the specified registry. For example, if the source
+container is `quay.io/biocontainers/bwa:0.7.13--1` and the build repository setting is `foo.com`, the resulting container
+name is `foo.com/biocontainers/bwa:0.7.13--1`.
+
+:::{tip}
+When using a path prefix in the target registry name, it will be prepended to the resulting container name. For example,
+having `quay.io/biocontainers/bwa:0.7.13--1` as source container and `foo.com/bar` as build repository, the resulting
+container will be named `foo.com/bar/biocontainers/bwa:0.7.13--1`.
+:::
+
+The credentials to allow the push of  containers in the target repository need to be provided via the Seqera Platform
+credentials manager. The account used for this is specified by the `tower.accessToken` in the configuration above.
+
+### Container security scanning
+
+Wave enables the scanning of containers used in your pipelines for security vulnerabilities.
+If any issues are detected, it will trigger an execution error and provide a report.
+
+To enable this capability add the following settings to your Nextflow configuration file:
+
+```groovy
+wave.enabled = true
+wave.scan.mode = 'required'
+tower.accessToken = '<YOUR ACCESS TOKEN>'
+```
+
+Nextflow will only allow the use of containers with no security
+vulnerabilities when using these settings. You can define the level of accepted vulnerabilities using `wave.scan.allowedLevels`. For example:
+
+```
+wave.scan.allowedLevels = 'low,medium'
+```
+
+The above setting will allow the use of containers with *low* and *medium* vulnerabilities. Accepted values are `low`, `medium`, `high`, and `critical`. See [common vulnerabilities scoring system](https://en.wikipedia.org/wiki/Common_Vulnerability_Scoring_System) for more information about these levels.
+
+:::{note}
+Wave's security scanning applies to any container used in your pipeline, whether it was built by Wave or simply accessed through it. The security scan automatically expires after one week. If a container is accessed again after 7 days or more, the scan will be re-executed.
+:::
+
 ### Run pipelines using Fusion file system
 
 Wave containers allows you to run your containerised workflow with the {ref}`fusion-page`.
diff --git a/docs/workflow.md b/docs/workflow.md
index bc87b38f80..bfc99c1f8d 100644
--- a/docs/workflow.md
+++ b/docs/workflow.md
@@ -2,75 +2,44 @@
 
 # Workflows
 
-In Nextflow, a **workflow** is a composition of processes and dataflow logic (i.e. channels and operators).
+In Nextflow, a **workflow** is a function that is specialized for composing processes and dataflow logic (i.e. channels and operators).
 
-The workflow definition starts with the keyword `workflow`, followed by an optional name, and finally the workflow body delimited by curly braces. A basic workflow looks like the following example:
+A script can define up to one *entry workflow*, which does not have a name and serves as the entrypoint of the script:
 
-```groovy
+```nextflow
 workflow {
-    foo()
-}
-```
-
-Where `foo` could be a function, a process, or another workflow.
-
-Workflows are *lazily executed*, which means that Nextflow parses the entire workflow structure first, and then executes the entire workflow at once. The order in which a task is executed is determined only by its dependencies, so a task will be executed as soon as all of its required inputs are available.
-
-The syntax of a workflow is defined as follows:
-
-```groovy
-workflow [ name ] {
-
-    take:
-    < workflow inputs >
-
-    main:
-    < dataflow statements >
-
-    emit:
-    < workflow outputs >
-
+    Channel.of('Bonjour', 'Ciao', 'Hello', 'Hola')
+        | map { v -> "$v world!" }
+        | view
 }
 ```
 
-:::{tip}
-The `main:` label can be omitted if there are no `take:` or `emit:` blocks.
-:::
-
-:::{note}
-Workflows were introduced in DSL2. If you are still using DSL1, see the {ref}`dsl1-page` page to learn how to migrate your Nextflow pipelines to DSL2.
-:::
-
-## Implicit workflow
-
-A script can define a single workflow without a name (also known as the *implicit workflow*), which is the default entrypoint of the script. The `-entry` command line option can be used to execute a different workflow as the entrypoint at runtime.
+A *named workflow*, on the other hand, is a workflow that can be called from other workflows:
 
-:::{note}
-Implicit workflow definitions are ignored when a script is included as a module. This way, a script can be written such that it can be either imported as a module or executed as a pipeline.
-:::
-
-## Named workflows
-
-A named workflow is a workflow that can be invoked from other workflows. For example:
-
-```groovy
-workflow my_pipeline {
+```nextflow
+workflow my_workflow {
     foo()
     bar( foo.out.collect() )
 }
 
 workflow {
-    my_pipeline()
+    my_workflow()
 }
 ```
 
-The above snippet defines a workflow named `my_pipeline`, that can be invoked from another workflow as `my_pipeline()`, just like any other function or process.
+The above example defines a workflow named `my_workflow` which can be called from another workflow as `my_workflow()`. Both `foo` and `bar` could be any other process or workflow.
+
+See {ref}`syntax-workflow` for a full description of the workflow syntax.
 
-## Using variables and params
+:::{note}
+Workflows were introduced in DSL2. If you are still using DSL1, see {ref}`dsl1-page` for more information about how to migrate your Nextflow pipelines to DSL2.
+:::
 
-A workflow can access any variable or parameter defined in the global scope:
+## Using parameters
 
-```groovy
+Parameters can be defined in the script with a default value that can be overridden from the CLI, params file, or config file. Params should only be used by the entry workflow:
+
+```nextflow
 params.data = '/some/data/file'
 
 workflow {
@@ -81,16 +50,16 @@ workflow {
 }
 ```
 
-:::{tip}
-The use of global variables and params in named workflows is discouraged because it breaks the modularity of the workflow. As a best practice, every workflow input should be explicitly defined as such in the `take:` block, and params should only be used in the implicit workflow.
+:::{note}
+While params can also be used by named workflows, this practice is discouraged. Named workflows should receive their inputs explicitly through the `take:` section.
 :::
 
 ## Workflow inputs (`take`)
 
-A workflow can declare one or more input channels using the `take` keyword. For example:
+The `take:` section is used to declare workflow inputs:
 
-```groovy
-workflow my_pipeline {
+```nextflow
+workflow my_workflow {
     take:
     data1
     data2
@@ -101,24 +70,20 @@ workflow my_pipeline {
 }
 ```
 
-:::{warning}
-When the `take` keyword is used, the beginning of the workflow body must be defined with the `main` keyword.
-:::
-
-Inputs can be specified like arguments when invoking the workflow:
+Inputs can be specified like arguments when calling the workflow:
 
-```groovy
+```nextflow
 workflow {
-    my_pipeline( channel.from('/some/data') )
+    my_workflow( Channel.of('/some/data') )
 }
 ```
 
 ## Workflow outputs (`emit`)
 
-A workflow can declare one or more output channels using the `emit` keyword. For example:
+The `emit:` section is used to declare workflow outputs:
 
-```groovy
-workflow my_pipeline {
+```nextflow
+workflow my_workflow {
     main:
     foo(data)
     bar(foo.out)
@@ -128,14 +93,12 @@ workflow my_pipeline {
 }
 ```
 
-When invoking the workflow, the output channel(s) can be accessed using the `out` property, i.e. `my_pipeline.out`. When multiple output channels are declared, use the array bracket notation or the assignment syntax to access each output channel as described for [process outputs](#process-outputs).
+When calling the workflow, the output can be accessed using the `out` property, i.e. `my_workflow.out`.
 
-### Named outputs
+If an output is assigned to a name, the name can be used to reference the output from the calling workflow. For example:
 
-If an output channel is assigned to an identifier in the `emit` block, the identifier can be used to reference the channel from the calling workflow. For example:
-
-```groovy
-workflow my_pipeline {
+```nextflow
+workflow my_workflow {
     main:
     foo(data)
     bar(foo.out)
@@ -145,18 +108,22 @@ workflow my_pipeline {
 }
 ```
 
-The result of the above workflow can be accessed using `my_pipeline.out.my_data`.
+The result of the above workflow can be accessed using `my_workflow.out.my_data`.
+
+:::{note}
+Every output must be assigned to a name when multiple outputs are declared.
+:::
 
 (workflow-process-invocation)=
 
-## Invoking processes
+## Calling processes and workflows
 
-A process can be invoked like a function in a workflow definition, passing the expected input channels like function arguments. For example:
+Processes and workflows are called like functions, passing their inputs as arguments:
 
-```groovy
+```nextflow
 process foo {
     output:
-    path 'foo.txt'
+    path 'foo.txt', emit: txt
 
     script:
     """
@@ -169,7 +136,7 @@ process bar {
     path x
 
     output:
-    path 'bar.txt'
+    path 'bar.txt', emit: txt
 
     script:
     """
@@ -177,140 +144,135 @@ process bar {
     """
 }
 
-workflow {
-    data = channel.fromPath('/some/path/*.txt')
+workflow flow {
+    take:
+    data
+
+    main:
     foo()
     bar(data)
 }
-```
 
-:::{warning}
-A process can be only be invoked once in a single workflow, however you can get around this restriction by using {ref}`module-aliases`.
-:::
-
-### Process composition
-
-Processes with matching input/output declarations can be composed so that the output of the first process is passed as input to the second process. The previous example can be rewritten as follows:
-
-```groovy
 workflow {
-    bar(foo())
+    data = Channel.fromPath('/some/path/*.txt')
+    flow(data)
 }
 ```
 
-### Process outputs
+Processes and workflows have a few extra rules for how they can be called:
 
-A process output can be accessed using the `out` attribute on the corresponding process object. For example:
+- Processes and workflows can only be called by workflows
 
-```groovy
-workflow {
-    foo()
-    bar(foo.out)
-    bar.out.view()
-}
-```
+- A given process or workflow can only be called once in a given workflow. To use a process or workflow multiple times in the same workflow, use {ref}`module-aliases`.
 
-When a process defines multiple output channels, each output can be accessed by index (`out[0]`, `out[1]`, etc.) or by name (see below).
+The "return value" of a process or workflow call is the process outputs or workflow emits, respectively. The return value can be assigned to a variable or passed into another call:
 
-The process output(s) can also be accessed like the return value of a function:
+```nextflow
+workflow flow {
+    take:
+    data
+
+    main:
+    bar_out = bar(foo(data))
+
+    emit:
+    bar_out
+}
 
-```groovy
 workflow {
-    f_out = foo()
-    (b1, b2) = bar(f_out)
-    b1.view()
+    data = Channel.fromPath('/some/path/*.txt')
+    flow_out = flow(data)
 }
 ```
 
-#### Named outputs
+Named outputs can be accessed as properties of the return value:
 
-The `emit` option can be added to the process output definition to assign a name identifier. This name can be used to reference the channel from the calling workflow. For example:
-
-```groovy
-process foo {
-    output:
-    path '*.bam', emit: samples_bam
+```nextflow
+workflow flow {
+    take:
+    data
 
-    '''
-    your_command --here
-    '''
-}
+    main:
+    foo_out = foo(data)
+    bar_out = bar(foo_out.txt)
 
-workflow {
-    foo()
-    foo.out.samples_bam.view()
+    emit:
+    bar = bar_out.txt
 }
-```
 
-When referencing a named output directly from the process invocation, you can use a more concise syntax:
-
-```groovy
 workflow {
-    ch_samples = foo().samples_bam
+    data = Channel.fromPath('/some/path/*.txt')
+    flow_out = flow(data)
+    bar_out = flow_out.bar
 }
 ```
 
-See {ref}`process outputs <process-additional-options>` for more details.
-
-#### Named stdout
-
-The `emit` option can also be used to name a `stdout` output. However, while process output options are usually prefixed with a comma, this is not the case for `stdout`. This is because `stdout` does not have an argument like other types.
+As a convenience, process and workflow outputs can also be accessed without first assigning to a variable, by using the `.out` property of the process or workflow name:
 
+```nextflow
+workflow flow {
+    take:
+    data
 
-```groovy
-process sayHello {
-    input:
-    val cheers
-
-    output:
-    stdout emit: verbiage
+    main:
+    foo(data)
+    bar(foo.out)
 
-    script:
-    """
-    echo -n $cheers
-    """
+    emit:
+    bar = bar.out
 }
 
 workflow {
-    things = channel.of('Hello world!', 'Yo, dude!', 'Duck!')
-    sayHello(things)
-    sayHello.out.verbiage.view()
+    data = Channel.fromPath('/some/path/*.txt')
+    flow(data)
+    flow.out.bar.view()
 }
 ```
 
-## Invoking workflows
+:::{note}
+Process named outputs are defined using the `emit` option on a process output. See {ref}`naming process outputs <process-naming-outputs>` for more information.
+:::
 
-Named workflows can be invoked and composed just like any other process or function.
+:::{note}
+Process and workflow outputs can also be accessed by index (e.g., `foo.out[0]`, `foo.out[1]`, etc.). Multiple outputs should instead be accessed by name.
+:::
 
-```groovy
+Workflows can be composed in the same way:
+
+```nextflow
 workflow flow1 {
-    take: data
+    take:
+    data
+
     main:
-        foo(data)
-        bar(foo.out)
+    foo(data)
+    bar(foo.out)
+
     emit:
-        bar.out
+    bar.out
 }
 
 workflow flow2 {
-    take: data
+    take:
+    data
+
     main:
-        foo(data)
-        baz(foo.out)
+    foo(data)
+    baz(foo.out)
+
     emit:
-        baz.out
+    baz.out
 }
 
 workflow {
-    take: data
-    main:
-        flow1(data)
-        flow2(flow1.out)
+    data = Channel.fromPath('/some/path/*.txt')
+    flow1(data)
+    flow2(flow1.out)
 }
 ```
 
 :::{note}
-Each workflow invocation has its own scope. As a result, the same process can be invoked in two different workflow scopes, like `foo` in the above snippet, which is used in both `flow1` and `flow2`. The workflow execution path, along with the process names, determines the *fully qualified process name* that is used to distinguish the different process invocations, i.e. `flow1:foo` and `flow2:foo` in the above example.
+The same process can be called in different workflows without using an alias, like `foo` in the above example, which is used in both `flow1` and `flow2`. The workflow call stack determines the *fully qualified process name*, which is used to distinguish the different process calls, i.e. `flow1:foo` and `flow2:foo` in the above example.
 :::
 
 :::{tip}
@@ -319,11 +281,13 @@ The fully qualified process name can be used as a {ref}`process selector <config
 
 ## Special operators
 
+The following operators have a special meaning when used in a workflow with process and workflow calls.
+
 ### Pipe `|`
 
-The `|` *pipe* operator can be used to compose Nextflow processes and operators. For example:
+The `|` *pipe* operator can be used to chain processes, operators, and workflows:
 
-```groovy
+```nextflow
 process foo {
     input:
     val data
@@ -336,30 +300,30 @@ process foo {
 }
 
 workflow {
-   channel.from('Hello','Hola','Ciao') | foo | map { it.toUpperCase() } | view
+    Channel.of('Hello','Hola','Ciao')
+        | foo
+        | map { v -> v.toUpperCase() }
+        | view
 }
 ```
 
-The above snippet defines a process named `foo` and invokes it with the `data` channel. The result is then piped to the {ref}`operator-map` operator, which converts each string to uppercase, and finally to the {ref}`operator-view` operator which prints it.
+The above snippet defines a process named `foo` and invokes it with the input channel. The result is then piped to the {ref}`operator-map` operator, which converts each string to uppercase, and finally to the {ref}`operator-view` operator which prints it.
 
-:::{tip}
-Statements can also be split across multiple lines for better readability:
+The same code can also be written as:
 
-```groovy
+```nextflow
 workflow {
-    channel.from('Hello','Hola','Ciao')
-      | foo
-      | map { it.toUpperCase() }
-      | view
+    ch1 = Channel.of('Hello','Hola','Ciao')
+    ch2 = foo( ch1 )
+    ch2.map { v -> v.toUpperCase() }.view()
 }
 ```
-:::
 
 ### And `&`
 
-The `&` *and* operator can be used to feed multiple processes with the same channel(s). For example:
+The `&` *and* operator can be used to call multiple processes in parallel with the same channel(s):
 
-```groovy
+```nextflow
 process foo {
     input:
     val data
@@ -383,16 +347,27 @@ process bar {
 }
 
 workflow {
-    channel.from('Hello')
-      | map { it.reverse() }
-      | (foo & bar)
-      | mix
-      | view
+    Channel.of('Hello')
+        | map { v -> v.reverse() }
+        | (foo & bar)
+        | mix
+        | view
 }
 ```
 
 In the above snippet, the initial channel is piped to the {ref}`operator-map` operator, which reverses the string value. Then, the result is passed to the processes `foo` and `bar`, which are executed in parallel. Each process outputs a channel, and the two channels are combined using the {ref}`operator-mix` operator. Finally, the result is printed using the {ref}`operator-view` operator.
 
+The same code can also be written as:
+
+```nextflow
+workflow {
+    ch = Channel.of('Hello').map { v -> v.reverse() }
+    ch_foo = foo(ch)
+    ch_bar = bar(ch)
+    ch_foo.mix(ch_bar).view()
+}
+```
+
 (workflow-output-def)=
 
 ## Publishing outputs
@@ -400,99 +375,73 @@ In the above snippet, the initial channel is piped to the {ref}`operator-map` op
 :::{versionadded} 24.04.0
 :::
 
+:::{versionchanged} 24.10.0
+A second preview version has been introduced. Read the [migration notes](#migrating-from-first-preview) for details.
+:::
+
 :::{note}
 This feature requires the `nextflow.preview.output` feature flag to be enabled.
 :::
 
-A script may define the set of outputs that should be published by the implicit workflow, known as the workflow output definition:
-
-```groovy
-workflow {
-    foo(bar())
-}
-
-output {
-    directory 'results'
-}
-```
-
-The output definition must be defined after the implicit workflow.
-
-### Publishing channels
+A workflow can publish outputs by sending channels to "publish targets" in the workflow `publish` section. Any channel in the workflow can be published, including process and subworkflow outputs. This approach is intended to replace the {ref}`publishDir <process-publishdir>` directive.
 
-Processes and workflows can each define a `publish` section which maps channels to publish targets. For example:
+Here is a basic example:
 
-```groovy
+```nextflow
 process foo {
     // ...
 
     output:
     path 'result.txt', emit: results
 
-    publish:
-    results >> 'foo'
+    // ...
+}
 
+process bar {
     // ...
 }
 
-workflow foobar {
+workflow {
     main:
     foo(data)
     bar(foo.out)
 
     publish:
-    foo.out >> 'foobar/foo'
-
-    emit:
-    bar.out
+    foo.out.results >> 'foo'
+    bar.out >> 'bar'
 }
 ```
 
-In the above example, the output `results` of process `foo` is published to the target `foo/` by default. However, when the workflow `foobar` invokes process `foo`, it publishes `foo.out` (i.e. `foo.out.results`) to the target `foobar/foo/`, overriding the default target defined by `foo`.
+In the above example, the `results` output of process `foo` is published to the target `foo`, and all outputs of process `bar` are published to the target `bar`.
 
-In a process, any output with an `emit` name can be published. In a workflow, any channel defined in the workflow, including process and subworkflow outputs, can be published.
+A "publish target" is simply a name that identifies a group of related outputs. How these targets are saved into a directory structure is described in the next section.
 
-:::{note}
-If the publish source is a process/workflow output (e.g. `foo.out`) with multiple channels, each channel will be published. Individual output channels can also be published by index or name (e.g. `foo.out[0]` or `foo.out.results`).
+:::{tip}
+A workflow can override the publish targets of a subworkflow by "re-publishing" the same channels to a different target. However, the best practice is to define all publish targets in the entry workflow, so that all publish targets are defined in one place at the top-level.
 :::
 
-As shown in the example, workflows can override the publish targets of process and subworkflow outputs. This way, each process and workflow can define some sensible defaults for publishing, which can be overridden by calling workflows as needed.
+### Output directory
 
-By default, all files emitted by the channel will be published into the specified directory. If a channel emits list values, any files in the list (including nested lists) will also be published. For example:
+The top-level output directory of a workflow run can be set using the `-output-dir` command-line option or the `outputDir` config option:
 
-```groovy
-workflow {
-    ch_samples = Channel.of(
-        [ [id: 'sample1'], file('sample1.txt') ]
-    )
-
-    publish:
-    ch_samples >> 'samples' // sample1.txt will be published
-}
+```bash
+nextflow run main.nf -output-dir 'my-results'
 ```
 
-### Publish directory
-
-The `directory` statement is used to set the top-level publish directory of the workflow:
-
 ```groovy
-output {
-    directory 'results'
-
-    // ...
-}
+// nextflow.config
+outputDir = 'my-results'
 ```
 
-It is optional, and it defaults to the launch directory (`workflow.launchDir`). Published files will be saved within this directory.
-
-### Publish targets
+It defaults to `results` in the launch directory. All published outputs will be saved into this directory.
 
-A publish target is a name with a specific publish configuration. By default, when a channel is published to a target in the `publish:` section of a process or workflow, the target name is used as the publish path.
+Each publish target is saved into a subdirectory of the output directory. By default, the target name is used as the directory name.
 
-For example, given the following output definition:
+For example, given the following publish targets:
 
-```groovy
+```nextflow
 workflow {
+    main:
     ch_foo = foo()
     ch_bar = bar(ch_foo)
 
@@ -500,10 +449,6 @@ workflow {
     ch_foo >> 'foo'
     ch_bar >> 'bar'
 }
-
-output {
-    directory 'results'
-}
 ```
 
 The following directory structure will be created:
@@ -516,130 +461,132 @@ results/
     └── ...
 ```
 
-:::{note}
-The trailing slash in the target name is not required; it is only used to denote that the target name is intended to be used as the publish path.
-:::
-
 :::{warning}
-The target name must not begin with a slash (`/`), it should be a relative path name.
+Target names cannot begin or end with a slash (`/`).
 :::
 
-Workflows can also disable publishing for specific channels by redirecting them to `null`:
+By default, all files emitted by a published channel will be published into the specified directory. If a channel emits list values, each file in the list (including nested lists) will be published. For example:
 
-```groovy
+```nextflow
 workflow {
-    ch_foo = foo()
+    main:
+    ch_samples = Channel.of(
+        [ [id: 'foo'], [ file('1.txt'), file('2.txt') ] ]
+    )
 
     publish:
-    ch_foo >> (params.save_foo ? 'foo' : null)
+    ch_samples >> 'samples' // 1.txt and 2.txt will be published
 }
 ```
 
-Publish targets can be customized in the output definition using a set of options similar to the {ref}`process-publishdir` directive.
-
-For example:
+A workflow can also disable publishing for a specific channel by redirecting it to `null`:
 
-```groovy
-output {
-    directory 'results'
-    mode 'copy'
+```nextflow
+workflow {
+    main:
+    ch_foo = foo()
 
-    'foo' {
-        mode 'link'
-    }
+    publish:
+    ch_foo >> (params.save_foo ? 'foo' : null)
 }
 ```
 
-In this example, all files will be copied by default, and files published to `foo/` will be hard-linked, overriding the default option.
+### Customizing outputs
 
-Available options:
+The output directory structure can be customized further in the "output block", which can be defined alongside an entry workflow. The output block consists of "target" blocks, which can be used to customize specific targets.
 
-`contentType`
-: *Currently only supported for S3.*
-: Specify the media type a.k.a. [MIME type](https://developer.mozilla.org/en-US/docs/Web/HTTP/Basics_of_HTTP/MIME_Types) of published files (default: `false`). Can be a string (e.g. `'text/html'`), or `true` to infer the content type from the file extension.
+For example:
 
-`enabled`
-: Enable or disable publishing (default: `true`).
+```nextflow
+workflow {
+    // ...
+}
 
-`ignoreErrors`
-: When `true`, the workflow will not fail if a file can't be published for some reason (default: `false`).
+output {
+    'foo' {
+        enabled params.save_foo
+        path 'intermediates/foo'
+    }
 
-`mode`
-: The file publishing method (default: `'symlink'`). The following options are available:
+    'bar' {
+        mode 'copy'
+    }
+}
+```
 
-  `'copy'`
-  : Copy each file into the output directory.
+This output block has the following effect:
 
-  `'copyNoFollow'`
-  : Copy each file into the output directory without following symlinks, i.e. only the link is copied.
+- The target `foo` will be published only if `params.save_foo` is enabled, and it will be published to a different path within the output directory.
 
-  `'link'`
-  : Create a hard link in the output directory for each file.
+- The target `bar` will publish files via copy instead of symlink.
 
-  `'move'`
-  : Move each file into the output directory.
-  : Should only be used for files which are not used by downstream processes in the workflow.
+See [Reference](#reference) for all available directives in the output block.
 
-  `'rellink'`
-  : Create a relative symbolic link in the output directory for each file.
+:::{tip}
+The output block is only needed if you want to customize the behavior of specific targets. If you are satisfied with the default behavior and don't need to customize anything, the output block can be omitted.
+:::
 
-  `'symlink'`
-  : Create an absolute symbolic link in the output directory for each output file.
+### Dynamic publish path
 
-`overwrite`
-: When `true` any existing file in the specified folder will be overwritten (default: `'standard'`). The following options are available:
+The `path` directive in a target block can also be a closure which defines a custom publish path for each channel value:
 
-  `false`
-  : Never overwrite existing files.
+```nextflow
+workflow {
+    main:
+    ch_fastq = Channel.of( [ [id: 'SAMP1'], file('1.fastq'), file('2.fastq') ] )
 
-  `true`
-  : Always overwrite existing files.
+    publish:
+    ch_fastq >> 'fastq'
+}
 
-  `'deep'`
-  : Overwrite existing files when the file content is different.
+output {
+    'fastq' {
+        path { meta, fastq_1, fastq_2 -> "fastq/${meta.id}" }
+    }
+}
+```
 
-  `'lenient'`
-  : Overwrite existing files when the file size is different.
+The above example will publish each channel value to a different subdirectory. In this case, each pair of FASTQ files will be published to a subdirectory based on the sample ID.
 
-  `'standard'`
-  : Overwrite existing files when the file size or last modified timestamp is different.
+The closure can even define a different path for each individual file by returning an inner closure, similar to the `saveAs` option of the {ref}`publishDir <process-publishdir>` directive:
 
-`path`
-: Specify the publish path relative to the output directory (default: the target name). Can only be specified within a target definition.
+```nextflow
+output {
+    'fastq' {
+        path { meta, fastq_1, fastq_2 ->
+            { file -> "fastq/${meta.id}/${file.baseName}" }
+        }
+    }
+}
+```
 
-`storageClass`
-: *Currently only supported for S3.*
-: Specify the storage class for published files.
+The inner closure will be applied to each file in the channel value, in this case `fastq_1` and `fastq_2`.
 
-`tags`
-: *Currently only supported for S3.*
-: Specify arbitrary tags for published files. For example:
-  ```groovy
-  tags FOO: 'hello', BAR: 'world'
-  ```
+:::{tip}
+A mapping closure should usually have only one parameter. However, if the incoming values are tuples, the closure can specify a parameter for each tuple element for more convenient access, also known as "destructuring" or "unpacking".
+:::
 
 ### Index files
 
-A publish target can create an index file of the values that were published. An index file is a useful way to save the metadata associated with files, and is more flexible than encoding metadata in the file path. Currently only CSV files are supported.
+A publish target can create an index file of the values that were published. An index file preserves the structure of channel values, including metadata, which is simpler than encoding this information with directories and file names. The index file can be CSV (`.csv`) or JSON (`.json`).
 
 For example:
 
-```groovy
+```nextflow
 workflow {
-    ch_foo = Channel.of(
-        [id: 1, name: 'foo 1'],
-        [id: 2, name: 'foo 2'],
-        [id: 3, name: 'foo 3']
+    main:
+    ch_fastq = Channel.of(
+        [ [id: 1, name: 'sample 1'], '1a.fastq', '1b.fastq' ],
+        [ [id: 2, name: 'sample 2'], '2a.fastq', '2b.fastq' ],
+        [ [id: 3, name: 'sample 3'], '3a.fastq', '3b.fastq' ]
     )
 
     publish:
-    ch_foo >> 'foo'
+    ch_fastq >> 'fastq'
 }
 
 output {
-    directory 'results'
-
-    'foo' {
+    'fastq' {
         index {
             path 'index.csv'
         }
@@ -647,36 +594,75 @@ output {
 }
 ```
 
-The above example will write the following CSV file to `results/foo/index.csv`:
+The above example will write the following CSV file to `results/fastq/index.csv`:
 
 ```csv
-"id","name"
-"1","foo 1"
-"2","foo 2"
-"3","foo 3"
+"id","name","fastq_1","fastq_2"
+"1","sample 1","results/fastq/1a.fastq","results/fastq/1b.fastq"
+"2","sample 2","results/fastq/2a.fastq","results/fastq/2b.fastq"
+"3","sample 3","results/fastq/3a.fastq","results/fastq/3b.fastq"
 ```
 
-You can customize the index file by specifying options in a block, for example:
+You can customize the index file with additional directives, for example:
 
-```groovy
+```nextflow
 index {
     path 'index.csv'
-    header ['name', 'extra_option']
+    header ['id', 'fastq_1', 'fastq_1']
     sep '\t'
-    mapper { val -> val + [extra_option: 'bar'] }
+    mapper { meta, fq_1, fq_2 -> meta + [fastq_1: fq_1, fastq_2: fq_2] }
 }
 ```
 
-The following options are available:
+This example will produce the same index file as above, but with the `name` column removed and with tabs instead of commas.
+
+See [Reference](#reference) for the list of available index directives.
+
+### Migrating from first preview
 
-`header`
-: When `true`, the keys of the first record are used as the column names (default: `false`). Can also be a list of column names.
+The first preview of workflow publishing was introduced in 24.04. The second preview, introduced in 24.10, made the following breaking changes:
 
-`mapper`
-: Closure which defines how to transform each published value into a CSV record. The closure should return a list or map. By default, no transformation is applied.
+- The process `publish:` section has been removed. Channels should be published only in workflows, ideally the entry workflow.
+
+- The `directory` output directive has been replaced with the `outputDir` config option and `-output-dir` command line option, which is `results` by default. The other directives such as `mode` have been replaced with config options under `workflow.output.*`.
+
+  In other words, only target blocks can be specified in the output block, but target blocks can still specify directives such as `mode`.
+
+- Target names cannot begin or end with a slash (`/`);
+
+### Reference
+
+The following directives are available in a target block:
+
+`index`
+: Create an index file which will contain a record of each published value.
+
+  The following directives are available in an index definition:
+
+  `header`
+  : When `true`, the keys of the first record are used as the column names (default: `false`). Can also be a list of column names. Only used for `csv` files.
+
+  `mapper`
+  : Closure which defines how to transform each published value into a record. The closure should return a list or map. By default, no transformation is applied.
+
+  `path`
+  : The name of the index file relative to the target path (required). Can be a `csv` or `json` file.
+
+  `sep`
+  : The character used to separate values (default: `','`). Only used for `csv` files.
 
 `path`
-: The name of the index file relative to the target path (required).
+: Specify the publish path relative to the output directory (default: the target name). Can be a path, a closure that defines a custom directory for each published value, or a closure that defines a custom path for each individual file.
 
-`sep`
-: The character used to separate values (default: `','`).
+Additionally, the following options from the {ref}`workflow <config-workflow>` config scope can be specified as directives:
+- `contentType`
+- `enabled`
+- `ignoreErrors`
+- `mode`
+- `overwrite`
+- `storageClass`
+- `tags`
+
+:::{note}
+Similarly to process directives vs {ref}`process <config-process>` config options, directives in the `output` block are specified without an equals sign (`=`).
+:::
diff --git a/docs/working-with-files.md b/docs/working-with-files.md
new file mode 100644
index 0000000000..aad769be96
--- /dev/null
+++ b/docs/working-with-files.md
@@ -0,0 +1,256 @@
+(working-with-files)=
+
+# Working with files
+
+## Opening files
+
+To access and work with files, use the `file()` method, which returns a file system object given a file path string:
+
+```nextflow
+myFile = file('some/path/to/my_file.file')
+```
+
+The `file()` method can reference both files and directories, depending on what the string path refers to in the file system.
+
+When using the wildcard characters `*`, `?`, `[]` and `{}`, the argument is interpreted as a [glob](http://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob) path matcher and the `file()` method returns a list object holding the paths of files whose names match the specified pattern, or an empty list if no match is found:
+
+```nextflow
+listOfFiles = file('some/path/*.fa')
+```
+
+:::{note}
+The `file()` method does not return a list if only one file is matched. Use the `files()` method to always return a list.
+:::
+
+:::{note}
+A double asterisk (`**`) in a glob pattern works like `*` but also searches through subdirectories.
+:::
+
+By default, wildcard characters do not match directories or hidden files. For example, if you want to include hidden files in the result list, enable the `hidden` option:
+
+```nextflow
+listWithHidden = file('some/path/*.fa', hidden: true)
+```
+
+:::{note}
+To compose paths, instead of string interpolation, use the `resolve()` method or the `/` operator:
+
+```nextflow
+def dir = file('s3://bucket/some/data/path')
+def sample1 = dir.resolve('sample.bam')         // correct
+def sample2 = dir / 'sample.bam'
+def sample3 = file("$dir/sample.bam")           // correct (but verbose)
+def sample4 = "$dir/sample.bam"                 // incorrect
+```
+:::
+
+## Getting file attributes
+
+The `file()` method returns a [Path](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/file/Path.html), which has several methods for retrieving metadata about the file:
+
+```nextflow
+def path = file('/some/path/file.txt')
+
+assert path.baseName == 'file'
+assert path.extension == 'txt'
+assert path.name == 'file.txt'
+assert path.parent == '/some/path'
+```
+
+:::{tip}
+When calling an object method, any method that looks like `get*()` can also be accessed as a field. For example, `path.getName()` is equivalent to `path.name`, `path.getBaseName()` is equivalent to `path.baseName`, and so on.
+:::
+
+See the {ref}`stdlib-types-path` reference for the list of available methods.
+
+## Reading and writing
+
+### Reading and writing an entire file
+
+Given a file variable, created with the `file()` method as shown previously, reading a file is as easy as getting the file's `text` property, which returns the file content as a string:
+
+```nextflow
+print myFile.text
+```
+
+Similarly, you can save a string to a file by assigning it to the file's `text` property:
+
+```nextflow
+myFile.text = 'Hello world!'
+```
+
+Binary data can managed in the same way, just using the file property `bytes` instead of `text`. Thus, the following example reads the file and returns its content as a byte array:
+
+```nextflow
+binaryContent = myFile.bytes
+```
+
+Or you can save a byte array to a file:
+
+```nextflow
+myFile.bytes = binaryContent
+```
+
+:::{note}
+The above assignment overwrites any existing file contents, and implicitly creates the file if it doesn't exist.
+:::
+
+:::{warning}
+The above methods read and write the **entire** file contents at once, in a single variable or buffer. For this reason, when dealing with large files it is recommended that you use a more memory efficient approach, such as reading/writing a file line by line or using a fixed size buffer.
+:::
+
+### Appending to a file
+
+In order to append a string value to a file without erasing existing content, you can use the `append()` method:
+
+```nextflow
+myFile.append('Add this line\n')
+```
+
+Or use the left shift operator, a more idiomatic way to append text content to a file:
+
+```nextflow
+myFile << 'Add a line more\n'
+```
+
+### Reading a file line by line
+
+In order to read a text file line by line you can use the method `readLines()` provided by the file object, which returns the file content as a list of strings:
+
+```nextflow
+myFile = file('some/my_file.txt')
+allLines = myFile.readLines()
+for( line : allLines ) {
+    println line
+}
+```
+
+This can also be written in a more idiomatic syntax:
+
+```nextflow
+file('some/my_file.txt')
+    .readLines()
+    .each { println it }
+```
+
+:::{warning}
+The method `readLines()` reads the **entire** file at once and returns a list containing all the lines. For this reason, do not use it to read big files.
+:::
+
+To process a big file, use the method `eachLine()`, which reads only a single line at a time into memory:
+
+```nextflow
+count = 0
+myFile.eachLine { str ->
+    println "line ${count++}: $str"
+}
+```
+
+### Advanced file reading
+
+The classes `Reader` and `InputStream` provide fine-grained control for reading text and binary files, respectively.
+
+The method `newReader()` creates a [Reader](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/Reader.html) object for the given file that allows you to read the content as single characters, lines or arrays of characters:
+
+```nextflow
+myReader = myFile.newReader()
+String line
+while( line = myReader.readLine() ) {
+    println line
+}
+myReader.close()
+```
+
+The method `withReader()` works similarly, but automatically calls the `close()` method for you when you have finished processing the file. So, the previous example can be written more simply as:
+
+```nextflow
+myFile.withReader {
+    String line
+    while( line = it.readLine() ) {
+        println line
+    }
+}
+```
+
+The methods `newInputStream()` and `withInputStream()` work similarly. The main difference is that they create an [InputStream](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/InputStream.html) object useful for writing binary data.
+
+See the {ref}`stdlib-types-path` reference for the list of available methods.
+
+### Advanced file writing
+
+The `Writer` and `OutputStream` classes provide fine-grained control for writing text and binary files, respectively, including low-level operations for single characters or bytes, and support for big files.
+
+For example, given two file objects `sourceFile` and `targetFile`, the following code copies the first file's content into the second file, replacing all `U` characters with `X`:
+
+```nextflow
+sourceFile.withReader { source ->
+    targetFile.withWriter { target ->
+        String line
+        while( line=source.readLine() ) {
+            target << line.replaceAll('U','X')
+        }
+    }
+}
+```
+
+See the {ref}`stdlib-types-path` reference for the list of available methods.
+
+## Filesystem operations
+
+Methods for performing filesystem operations such as copying, deleting, and directory listing are documented in the {ref}`stdlib-types-path` reference.
+
+### Listing directories
+
+The simplest way to list a directory is to use `list()` or `listFiles()`, which return a collection of first-level elements (files and directories) of a directory:
+
+```nextflow
+for( def file : file('any/path').list() ) {
+    println file
+}
+```
+
+Additionally, the `eachFile()` method allows you to iterate through the first-level elements only (just like `listFiles()`). As with other `each*()` methods, `eachFile()` takes a closure as a parameter:
+
+```nextflow
+myDir.eachFile { item ->
+    if( item.isFile() ) {
+        println "${item.getName()} - size: ${item.size()}"
+    }
+    else if( item.isDirectory() ) {
+        println "${item.getName()} - DIR"
+    }
+}
+```
+
+### Copying files
+
+In general, you should not need to manually copy files, because Nextflow will automatically stage files in and out of the task environment based on the definition of process inputs and outputs. Ideally, any operation which transforms files should be encapsulated in a process, in order to leverage Nextflow's staging capabilities as much as possible.
+
+## Remote files
+
+Nextflow can work with many kinds of remote files and objects using the same interface as for local files. The following protocols are supported:
+
+- HTTP(S) / FTP (`http://`, `https://`, `ftp://`)
+- Amazon S3 (`s3://`)
+- Azure Blob Storage (`az://`)
+- Google Cloud Storage (`gs://`)
+
+To reference a remote file, simple specify the URL when opening the file:
+
+```nextflow
+pdb = file('http://files.rcsb.org/header/5FID.pdb')
+```
+
+You can then access it as a local file as described previously:
+
+```nextflow
+println pdb.text
+```
+
+:::{note}
+Not all operations are supported for all protocols. In particular, writing and directory listing are not supported for HTTP(S) and FTP paths.
+:::
+
+:::{note}
+Additional configuration may be required to work with cloud object storage (e.g. to authenticate with a private bucket). Refer to the respective page for each cloud storage provider for more information.
+:::
diff --git a/docs/your-first-script.md b/docs/your-first-script.md
index 6b8cfcf10a..b5101d4b9c 100644
--- a/docs/your-first-script.md
+++ b/docs/your-first-script.md
@@ -7,7 +7,7 @@
 This script defines two processes. The first splits a string into 6-character chunks, writing each one to a file with the prefix `chunk_`, and the second receives these files and transforms their contents to uppercase letters. The resulting strings are emitted on the `result` channel and the final output is printed by the `view` operator. Copy the following example into your favorite text editor and save it to a file named `tutorial.nf`:
 
 ```{literalinclude} snippets/your-first-script.nf
-:language: groovy
+:language: nextflow
 ```
 
 Execute the script by entering the following command in your terminal:
@@ -48,13 +48,14 @@ Nextflow keeps track of all the processes executed in your pipeline. If you modi
 
 For the sake of this tutorial, modify the `convertToUpper` process in the previous example, replacing the process script with the string `rev $x`, like so:
 
-```groovy
+```nextflow
 process convertToUpper {
   input:
     path x
   output:
     stdout
 
+  script:
   """
   rev $x
   """
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
index 09523c0e54..df97d72b8b 100644
--- a/gradle/wrapper/gradle-wrapper.properties
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.9-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.10.2-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
diff --git a/launch.sh b/launch.sh
index e2b18b0e0d..846eaf9eb6 100755
--- a/launch.sh
+++ b/launch.sh
@@ -66,13 +66,13 @@ fi
 JAVA_VER=$(echo "$JAVA_VER" | awk '/version/ {gsub(/"/, "", $3); print $3}')
 major=${BASH_REMATCH[1]}
 minor=${BASH_REMATCH[2]}
-version_check="^(1.8|9|10|11|12|13|14|15|16|17|18|19|20|21|22)"
+version_check="^(17|18|19|20|21|23)"
 if [[ ! $JAVA_VER =~ $version_check ]]; then
-    echo "Error: cannot find Java or it's a wrong version -- please make sure that Java 8 or higher is installed"
+    echo "Error: cannot find Java or it's a wrong version -- please make sure that Java 17 or higher is installed"
     exit 1
 fi
 JVM_ARGS+=" -Dfile.encoding=UTF-8 -XX:+TieredCompilation -XX:TieredStopAtLevel=1"
-[[ $JAVA_VER =~ ^(9|10|11|12|13|14|15|16|17|18|19|20|21|22) ]] && JVM_ARGS+=" --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED --add-opens=java.base/java.nio.file.spi=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED --add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED --add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED --add-opens=java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/sun.nio.fs=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED --add-opens=java.base/jdk.internal.misc=ALL-UNNAMED --add-opens=java.base/jdk.internal.vm=ALL-UNNAMED --add-opens=java.base/java.util.regex=ALL-UNNAMED"
+JVM_ARGS+=" --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED --add-opens=java.base/java.nio.file.spi=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED --add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED --add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED --add-opens=java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/sun.nio.fs=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED --add-opens=java.base/jdk.internal.misc=ALL-UNNAMED --add-opens=java.base/jdk.internal.vm=ALL-UNNAMED --add-opens=java.base/java.util.regex=ALL-UNNAMED"
 [[ $NXF_ENABLE_VIRTUAL_THREADS == 'true' ]] && [[ "$JAVA_VER" =~ ^(19|20) ]] && JVM_ARGS+=" --enable-preview"
 [[ "$JAVA_VER" =~ ^(21) ]] && [[ ! "$NXF_ENABLE_VIRTUAL_THREADS" ]] && NXF_ENABLE_VIRTUAL_THREADS=true
 
diff --git a/modules/nextflow/build.gradle b/modules/nextflow/build.gradle
index e01d56d674..867d5e2c5a 100644
--- a/modules/nextflow/build.gradle
+++ b/modules/nextflow/build.gradle
@@ -1,5 +1,5 @@
 plugins {
-    id "com.github.johnrengelman.shadow" version "8.1.1"
+    id "com.gradleup.shadow" version "8.3.5"
 }
 apply plugin: 'groovy'
 apply plugin: 'application'
@@ -20,12 +20,12 @@ compileGroovy {
 dependencies {
     api(project(':nf-commons'))
     api(project(':nf-httpfs'))
-    api "org.apache.groovy:groovy:4.0.22"
-    api "org.apache.groovy:groovy-nio:4.0.22"
-    api "org.apache.groovy:groovy-xml:4.0.22"
-    api "org.apache.groovy:groovy-json:4.0.22"
-    api "org.apache.groovy:groovy-templates:4.0.22"
-    api "org.apache.groovy:groovy-yaml:4.0.22"
+    api "org.apache.groovy:groovy:4.0.24"
+    api "org.apache.groovy:groovy-nio:4.0.24"
+    api "org.apache.groovy:groovy-xml:4.0.24"
+    api "org.apache.groovy:groovy-json:4.0.24"
+    api "org.apache.groovy:groovy-templates:4.0.24"
+    api "org.apache.groovy:groovy-yaml:4.0.24"
     api "org.slf4j:jcl-over-slf4j:2.0.7"
     api "org.slf4j:jul-to-slf4j:2.0.7"
     api "org.slf4j:log4j-over-slf4j:2.0.7"
@@ -35,11 +35,11 @@ dependencies {
     api("ch.artecat.grengine:grengine:3.0.2") { exclude group: 'org.codehaus.groovy' }
     api "commons-lang:commons-lang:2.6"
     api "commons-codec:commons-codec:1.15"
-    api "commons-io:commons-io:2.11.0"
+    api "commons-io:commons-io:2.15.1"
     api "com.beust:jcommander:1.35"
     api("com.esotericsoftware.kryo:kryo:2.24.0") { exclude group: 'com.esotericsoftware.minlog', module: 'minlog' }
     api('org.iq80.leveldb:leveldb:0.12')
-    api('org.eclipse.jgit:org.eclipse.jgit:6.10.0.202406032230-r')
+    api('org.eclipse.jgit:org.eclipse.jgit:7.1.0.202411261347-r')
     api ('javax.activation:activation:1.1.1')
     api ('javax.mail:mail:1.4.7')
     api ('org.yaml:snakeyaml:2.2')
@@ -47,17 +47,17 @@ dependencies {
     api 'jline:jline:2.9'
     api 'org.pf4j:pf4j:3.12.0'
     api 'dev.failsafe:failsafe:3.1.0'
-    api 'org.bouncycastle:bcprov-ext-jdk15on:1.70'
-    api 'org.bouncycastle:bcpkix-jdk15on:1.70'
+    api 'org.bouncycastle:bcprov-ext-jdk18on:1.78.1'
+    api 'org.bouncycastle:bcpkix-jdk18on:1.78.1'
 
     testImplementation 'org.subethamail:subethasmtp:3.1.7'
 
     // test configuration
-    testFixturesApi ("org.apache.groovy:groovy-test:4.0.22") { exclude group: 'org.apache.groovy' }
-    testFixturesApi ("cglib:cglib-nodep:3.3.0")
-    testFixturesApi ("org.objenesis:objenesis:3.2")
-    testFixturesApi ("org.spockframework:spock-core:2.3-groovy-4.0") { exclude group: 'org.apache.groovy'; exclude group: 'net.bytebuddy' }
-    testFixturesApi ('org.spockframework:spock-junit4:2.3-groovy-4.0') { exclude group: 'org.apache.groovy'; exclude group: 'net.bytebuddy' }
+    testFixturesApi ("org.apache.groovy:groovy-test:4.0.24") { exclude group: 'org.apache.groovy' }
+    testFixturesApi ("org.objenesis:objenesis:3.4")
+    testFixturesApi ("net.bytebuddy:byte-buddy:1.14.17")
+    testFixturesApi ("org.spockframework:spock-core:2.3-groovy-4.0") { exclude group: 'org.apache.groovy' }
+    testFixturesApi ('org.spockframework:spock-junit4:2.3-groovy-4.0') { exclude group: 'org.apache.groovy' }
     testFixturesApi 'com.google.jimfs:jimfs:1.2'
 
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/NF.groovy b/modules/nextflow/src/main/groovy/nextflow/NF.groovy
index 4767e41d56..871de85271 100644
--- a/modules/nextflow/src/main/groovy/nextflow/NF.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/NF.groovy
@@ -64,6 +64,10 @@ class NF {
         NextflowMeta.instance.isStrictModeEnabled()
     }
 
+    static boolean isModuleBinariesEnabled() {
+        NextflowMeta.instance.isModuleBinariesEnabled()
+    }
+
     static boolean isOutputDefinitionEnabled() {
         NextflowMeta.instance.preview.output
     }
diff --git a/modules/nextflow/src/main/groovy/nextflow/Nextflow.groovy b/modules/nextflow/src/main/groovy/nextflow/Nextflow.groovy
index 3f1257a01c..e7dc15884c 100644
--- a/modules/nextflow/src/main/groovy/nextflow/Nextflow.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/Nextflow.groovy
@@ -57,6 +57,17 @@ class Nextflow {
 
     private static final Random random = new Random()
 
+    /**
+     * Get the value of an environment variable from the launch environment.
+     *
+     * @param name
+     *      The environment variable name to be referenced
+     * @return
+     *      The value associate with the specified variable name or {@code null} if the variable does not exist.
+     */
+    static String env(String name) {
+        return SysEnv.get(name)
+    }
 
     static private fileNamePattern( FilePatternSplitter splitter, Map opts ) {
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/NextflowMeta.groovy b/modules/nextflow/src/main/groovy/nextflow/NextflowMeta.groovy
index c45d8cecfe..37d6d5993b 100644
--- a/modules/nextflow/src/main/groovy/nextflow/NextflowMeta.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/NextflowMeta.groovy
@@ -35,6 +35,7 @@ class NextflowMeta {
     static trait Flags {
         abstract float dsl
         abstract boolean strict
+        abstract boolean moduleBinaries
     }
 
     @Slf4j
@@ -44,6 +45,7 @@ class NextflowMeta {
         boolean output
         boolean recursion
         boolean topic
+        boolean moduleBinaries
 
         @Deprecated
         void setDsl( float num ) {
@@ -78,6 +80,7 @@ class NextflowMeta {
     static class Features implements Flags {
         volatile float dsl
         boolean strict
+        boolean moduleBinaries
     }
 
     final VersionNumber version
@@ -110,6 +113,8 @@ class NextflowMeta {
             result.dsl = 2i
         if( isStrictModeEnabled() )
             result.strict = true
+        if( isModuleBinariesEnabled() )
+            result.moduleBinaries = true
         return result
     }
 
@@ -163,6 +168,14 @@ class NextflowMeta {
         enable.strict = mode
     }
 
+    boolean isModuleBinariesEnabled() {
+        return enable.moduleBinaries
+    }
+
+    void moduleBinaries(boolean mode) {
+        enable.moduleBinaries = mode
+    }
+
     static String checkDslMode(String script) {
         final matcher = DSL_DECLARATION.matcher(script)
         final mode = matcher.find() ? matcher.group(2) : null
diff --git a/modules/nextflow/src/main/groovy/nextflow/Session.groovy b/modules/nextflow/src/main/groovy/nextflow/Session.groovy
index 613a0246e1..f394245259 100644
--- a/modules/nextflow/src/main/groovy/nextflow/Session.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/Session.groovy
@@ -71,6 +71,7 @@ import nextflow.util.Barrier
 import nextflow.util.ConfigHelper
 import nextflow.util.Duration
 import nextflow.util.HistoryFile
+import nextflow.util.LoggerHelper
 import nextflow.util.NameGenerator
 import nextflow.util.SysHelper
 import nextflow.util.ThreadPoolManager
@@ -122,6 +123,11 @@ class Session implements ISession {
      */
     boolean resumeMode
 
+    /**
+     * The folder where workflow outputs are stored
+     */
+    Path outputDir
+
     /**
      * The folder where tasks temporary files are stored
      */
@@ -375,8 +381,11 @@ class Session implements ISession {
         // -- DAG object
         this.dag = new DAG()
 
+        // -- init output dir
+        this.outputDir = FileHelper.toCanonicalPath(config.outputDir ?: 'results')
+
         // -- init work dir
-        this.workDir = ((config.workDir ?: 'work') as Path).complete()
+        this.workDir = FileHelper.toCanonicalPath(config.workDir ?: 'work')
         this.setLibDir( config.libDir as String )
 
         // -- init cloud cache path
@@ -779,10 +788,11 @@ class Session implements ISession {
      */
     void abort(Throwable cause = null) {
         if( aborted ) return
-        if( !(cause instanceof ScriptCompilationException) )
+        if( cause !instanceof ScriptCompilationException )
             log.debug "Session aborted -- Cause: ${cause?.message ?: cause ?: '-'}"
         aborted = true
         error = cause
+        LoggerHelper.aborted = true
         try {
             // log the dataflow network status
             def status = dumpNetworkStatus()
@@ -828,6 +838,12 @@ class Session implements ISession {
 
     boolean isSuccess() { !aborted && !cancelled && !failOnIgnore }
 
+    boolean canSubmitTasks() {
+        // tasks should be submitted even when 'failOnIgnore' is set to true
+        // https://github.com/nextflow-io/nextflow/issues/5291
+        return !aborted && !cancelled
+    }
+
     void processRegister(TaskProcessor process) {
         log.trace ">>> barrier register (process: ${process.name})"
         processesBarrier.register(process)
@@ -863,7 +879,7 @@ class Session implements ISession {
     }
 
     boolean enableModuleBinaries() {
-        config.navigate('nextflow.enable.moduleBinaries', false) as boolean
+        NF.isModuleBinariesEnabled()
     }
 
     boolean failOnIgnore() {
@@ -1110,6 +1126,17 @@ class Session implements ISession {
         }
     }
 
+    void notifyWorkflowPublish(Object value) {
+        for( final observer : observers ) {
+            try {
+                observer.onWorkflowPublish(value)
+            }
+            catch( Exception e ) {
+                log.error "Failed to invoke observer on workflow publish: $observer", e
+            }
+        }
+    }
+
     void notifyFilePublish(Path destination, Path source=null) {
         def copy = new ArrayList<TraceObserver>(observers)
         for( TraceObserver observer : copy  ) {
diff --git a/modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy b/modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy
index b3c16b4af7..aa9f09c204 100644
--- a/modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy
@@ -550,23 +550,23 @@ class NextflowDSLImpl implements ASTTransformation {
             for( Statement stmt : block.statements ) {
                 if( stmt !instanceof ExpressionStatement ) {
                     syntaxError(stmt, "Invalid publish target definition")
-                    return     
+                    return
                 }
 
                 final stmtExpr = (ExpressionStatement)stmt
                 if( stmtExpr.expression !instanceof MethodCallExpression ) {
                     syntaxError(stmt, "Invalid publish target definition")
-                    return     
+                    return
                 }
 
                 final call = (MethodCallExpression)stmtExpr.expression
                 assert call.arguments instanceof ArgumentListExpression
 
-                // HACK: target definition is a method call with single closure argument
-                //       custom parser will be able to detect more elegantly
                 final targetArgs = (ArgumentListExpression)call.arguments
-                if( targetArgs.size() != 1 || targetArgs[0] !instanceof ClosureExpression )
-                    continue
+                if( targetArgs.size() != 1 || targetArgs[0] !instanceof ClosureExpression ) {
+                    syntaxError(stmt, "Invalid publish target definition")
+                    return
+                }
 
                 final targetName = call.method
                 final targetBody = (ClosureExpression)targetArgs[0]
@@ -633,11 +633,6 @@ class NextflowDSLImpl implements ASTTransformation {
                             }
                             break
 
-                        case 'publish':
-                            if( stm instanceof ExpressionStatement )
-                                convertPublishMethod( stm )
-                            break
-
                         case 'exec':
                             bodyLabel = currentLabel
                             iterator.remove()
@@ -1299,27 +1294,6 @@ class NextflowDSLImpl implements ASTTransformation {
             return false
         }
 
-        protected void convertPublishMethod(ExpressionStatement stmt) {
-            if( stmt.expression !instanceof BinaryExpression ) {
-                syntaxError(stmt, "Invalid process publish statement")
-                return
-            }
-
-            final binaryX = (BinaryExpression)stmt.expression
-            if( binaryX.operation.type != Types.RIGHT_SHIFT ) {
-                syntaxError(stmt, "Invalid process publish statement")
-                return
-            }
-
-            final left = binaryX.leftExpression
-            if( left !instanceof VariableExpression ) {
-                syntaxError(stmt, "Invalid process publish statement")
-                return
-            }
-
-            stmt.expression = callThisX('_publish_target', args(constX(((VariableExpression)left).name), binaryX.rightExpression))
-        }
-
         protected boolean isIllegalName(String name, ASTNode node) {
             if( name in RESERVED_NAMES ) {
                 unit.addError( new SyntaxException("Identifier `$name` is reserved for internal use", node.lineNumber, node.columnNumber+8) )
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdConfig.groovy
index 5ff2156b18..e120653127 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdConfig.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdConfig.groovy
@@ -41,6 +41,8 @@ class CmdConfig extends CmdBase {
 
     static final public NAME = 'config'
 
+    static final List<String> FORMATS = ['flat','properties','canonical','json','yaml']
+
     @Parameter(description = 'project name')
     List<String> args = []
 
@@ -50,10 +52,12 @@ class CmdConfig extends CmdBase {
     @Parameter(names=['-profile'], description = 'Choose a configuration profile')
     String profile
 
-    @Parameter(names = '-properties', description = 'Prints config using Java properties notation')
+    @Deprecated
+    @Parameter(names = '-properties', description = 'Prints config using Java properties notation (deprecated: use `-o properties` instead)')
     boolean printProperties
 
-    @Parameter(names = '-flat', description = 'Print config using flat notation')
+    @Deprecated
+    @Parameter(names = '-flat', description = 'Print config using flat notation (deprecated: use `-o flat` instead)')
     boolean printFlatten
 
     @Parameter(names = '-sort', description = 'Sort config attributes')
@@ -62,6 +66,9 @@ class CmdConfig extends CmdBase {
     @Parameter(names = '-value', description = 'Print the value of a config option, or fail if the option is not defined')
     String printValue
 
+    @Parameter(names = ['-o','-output'], description = 'Print the config using the specified format: canonical,properties,flat,json,yaml')
+    String outputFormat
+
     @Override
     String getName() { NAME }
 
@@ -79,13 +86,22 @@ class CmdConfig extends CmdBase {
         }
 
         if( printProperties && printFlatten )
-            throw new AbortOperationException("Option `-flat` and `-properties` conflicts")
+            throw new AbortOperationException("Option `-flat` and `-properties` conflicts each other")
 
         if ( printValue && printFlatten )
-            throw new AbortOperationException("Option `-value` and `-flat` conflicts")
+            throw new AbortOperationException("Option `-value` and `-flat` conflicts each other")
 
         if ( printValue && printProperties )
-            throw new AbortOperationException("Option `-value` and `-properties` conflicts")
+            throw new AbortOperationException("Option `-value` and `-properties` conflicts each other")
+
+        if( printValue && outputFormat )
+            throw new AbortOperationException("Option `-value` and `-output` conflicts each other")
+
+        if( printFlatten )
+            outputFormat = 'flat'
+
+        if( printProperties )
+            outputFormat = 'properties'
 
         final builder = new ConfigBuilder()
                 .setShowClosures(true)
@@ -97,18 +113,31 @@ class CmdConfig extends CmdBase {
 
         final config = builder.buildConfigObject()
 
-        if( printProperties ) {
+        if( printValue ) {
+            printValue0(config, printValue, stdout)
+        }
+        else if( outputFormat=='properties' ) {
             printProperties0(config, stdout)
         }
-        else if( printFlatten ) {
+        else if( outputFormat=='flat' ) {
             printFlatten0(config, stdout)
         }
-        else if( printValue ) {
-            printValue0(config, printValue, stdout)
+        else if( outputFormat=='yaml' ) {
+            printYaml0(config, stdout)
         }
-        else {
+        else if( outputFormat=='json') {
+            printJson0(config, stdout)
+        }
+        else if( !outputFormat || outputFormat=='canonical' ) {
             printCanonical0(config, stdout)
         }
+        else {
+            def msg = "Unknown output format: $outputFormat"
+            def suggest = FORMATS.closest(outputFormat)
+            if( suggest )
+                msg += " - did you mean '${suggest.first()}' instead?"
+            throw new AbortOperationException(msg)
+        }
 
         for( String msg : builder.warnings )
             log.warn(msg)
@@ -172,6 +201,13 @@ class CmdConfig extends CmdBase {
         config.writeTo( writer )
     }
 
+    @PackageScope void printJson0(ConfigObject config, OutputStream output) {
+        output << ConfigHelper.toJsonString(config, sort) << '\n'
+    }
+
+    @PackageScope void printYaml0(ConfigObject config, OutputStream output) {
+        output << ConfigHelper.toYamlString(config, sort)
+    }
 
     Path getBaseDir(String path) {
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdInspect.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdInspect.groovy
index 21582fc692..83aa249fb7 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdInspect.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdInspect.groovy
@@ -70,7 +70,7 @@ class CmdInspect extends CmdBase {
 
     @Override
     void run() {
-        ContainerInspectMode.activate(true)
+        ContainerInspectMode.activate(!concretize)
         // configure quiet mode
         LoggerHelper.setQuiet(true)
         // setup the target run command
@@ -91,19 +91,11 @@ class CmdInspect extends CmdBase {
     }
 
     protected void applyInspect(Session session) {
-        // disable wave await mode when running
-        if( session.config.wave instanceof Map )
-            checkWaveConfig(session.config.wave as Map)
         // run the inspector
-        new ContainersInspector(session.dag)
+        new ContainersInspector(session.dag, concretize)
                 .withFormat(format)
                 .withIgnoreErrors(ignoreErrors)
                 .printContainers()
     }
 
-    protected void checkWaveConfig(Map wave) {
-        if( wave.enabled && wave.freeze )
-            wave.dryRun = !concretize
-    }
-
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
index e5d18bdb87..5f6c904fe0 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
@@ -46,6 +46,7 @@ import nextflow.script.ScriptRunner
 import nextflow.util.CustomPoolFactory
 import nextflow.util.Duration
 import nextflow.util.HistoryFile
+import org.apache.commons.lang.StringUtils
 import org.fusesource.jansi.AnsiConsole
 import org.yaml.snakeyaml.Yaml
 /**
@@ -107,6 +108,9 @@ class CmdRun extends CmdBase implements HubOptions {
     @Parameter(names=['-test'], description = 'Test a script function with the name specified')
     String test
 
+    @Parameter(names=['-o', '-output-dir'], description = 'Directory where workflow outputs are stored')
+    String outputDir
+
     @Parameter(names=['-w', '-work-dir'], description = 'Directory where intermediate result files are stored')
     String workDir
 
@@ -416,12 +420,9 @@ class CmdRun extends CmdBase implements HubOptions {
 
     protected void launchInfo(ConfigMap config, ScriptFile scriptFile) {
         // -- determine strict mode
-        final defStrict = sysEnv.get('NXF_ENABLE_STRICT') ?: false
-        final strictMode = config.navigate('nextflow.enable.strict', defStrict)
-        if( strictMode ) {
-            log.debug "Enabling nextflow strict mode"
-            NextflowMeta.instance.strictMode(true)
-        }
+        detectStrictFeature(config, sysEnv)
+        // -- determine moduleBinary
+        detectModuleBinaryFeature(config)
         // -- determine dsl mode
         final dsl = detectDslMode(config, scriptFile.main.text, sysEnv)
         NextflowMeta.instance.enableDsl(dsl)
@@ -435,6 +436,24 @@ class CmdRun extends CmdBase implements HubOptions {
         printLaunchInfo(ver, repo, head, revision)
     }
 
+    static void detectModuleBinaryFeature(ConfigMap config) {
+        final moduleBinaries = config.navigate('nextflow.enable.moduleBinaries', false)
+        if( moduleBinaries ) {
+            log.debug "Enabling module binaries"
+            NextflowMeta.instance.moduleBinaries(true)
+        }
+    }
+
+    static void detectStrictFeature(ConfigMap config, Map sysEnv) {
+        final defStrict = sysEnv.get('NXF_ENABLE_STRICT') ?: false
+        log
+        final strictMode = config.navigate('nextflow.enable.strict', defStrict)
+        if( strictMode ) {
+            log.debug "Enabling nextflow strict mode"
+            NextflowMeta.instance.strictMode(true)
+        }
+    }
+
     protected void printLaunchInfo(String ver, String repo, String head, String revision) {
         if( launcher.options.ansiLog ){
             log.debug "${head} [$runName] DSL${ver} - revision: ${revision}"
@@ -670,6 +689,19 @@ class CmdRun extends CmdBase implements HubOptions {
         }
     }
 
+    static protected void addParam0(Map params, String key, Object value) {
+        if( key.contains('-') )
+            key = kebabToCamelCase(key)
+        params.put(key, value)
+    }
+
+    static protected String kebabToCamelCase(String str) {
+        final result = new StringBuilder()
+        str.split('-').eachWithIndex { String entry, int i ->
+            result << (i>0 ? StringUtils.capitalize(entry) : entry )
+        }
+        return result.toString()
+    }
 
     static protected parseParamValue(String str) {
         if ( SysEnv.get('NXF_DISABLE_PARAMS_TYPE_DETECTION') )
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
index 64531ae50e..ec60408ecb 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
@@ -654,6 +654,7 @@ class Launcher {
      * @param args The program options as specified by the user on the CLI
      */
     static void main(String... args)  {
+        LoggerHelper.bootstrapLogger()
         final status = new Launcher() .command(args) .run()
         if( status )
             System.exit(status)
diff --git a/modules/nextflow/src/main/groovy/nextflow/conda/CondaCache.groovy b/modules/nextflow/src/main/groovy/nextflow/conda/CondaCache.groovy
index 103b6afbb2..5ddd4734f8 100644
--- a/modules/nextflow/src/main/groovy/nextflow/conda/CondaCache.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/conda/CondaCache.groovy
@@ -22,6 +22,7 @@ import java.nio.file.Path
 import java.nio.file.Paths
 import java.util.concurrent.ConcurrentHashMap
 
+import com.google.common.hash.Hashing
 import groovy.transform.CompileStatic
 import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
@@ -33,7 +34,6 @@ import nextflow.util.CacheHelper
 import nextflow.util.Duration
 import nextflow.util.Escape
 import nextflow.util.TestOnly
-import org.yaml.snakeyaml.Yaml
 /**
  * Handle Conda environment creation and caching
  *
@@ -166,6 +166,18 @@ class CondaCache {
         str.endsWith('.txt') && !str.contains('\n')
     }
 
+    static protected String sipHash(CharSequence data) {
+        Hashing
+            .sipHash24()
+            .newHasher()
+            .putUnencodedChars(data)
+            .hash()
+            .toString()
+    }
+
+    static protected String sipHash(Path path) {
+        sipHash(path.toAbsolutePath().normalize().toString())
+    }
 
     /**
      * Get the path on the file system where store a Conda environment
@@ -188,11 +200,8 @@ class CondaCache {
             try {
                 final path = condaEnv as Path
                 content = path.text
-                final yaml = (Map)new Yaml().load(content)
-                if( yaml.name )
-                    name = yaml.name
-                else
-                    name = path.baseName
+                name = 'env-' + sipHash(path)
+
             }
             catch( NoSuchFileException e ) {
                 throw new IllegalArgumentException("Conda environment file does not exist: $condaEnv")
@@ -205,7 +214,7 @@ class CondaCache {
             try {
                 final path = condaEnv as Path
                 content = path.text
-                name = path.baseName
+                name = 'env-' + sipHash(path)
             }
             catch( NoSuchFileException e ) {
                 throw new IllegalArgumentException("Conda environment file does not exist: $condaEnv")
@@ -242,8 +251,8 @@ class CondaCache {
      * @return the conda environment prefix {@link Path}
      */
     @PackageScope
-    Path createLocalCondaEnv(String condaEnv) {
-        final prefixPath = condaPrefixPath(condaEnv)
+    Path createLocalCondaEnv(String condaEnv, Path prefixPath) {
+
         if( prefixPath.isDirectory() ) {
             log.debug "${binaryName} found local env for environment=$condaEnv; path=$prefixPath"
             return prefixPath
@@ -285,7 +294,8 @@ class CondaCache {
         def cmd
         if( isYamlFilePath(condaEnv) ) {
             final target = isYamlUriPath(condaEnv) ? condaEnv : Escape.path(makeAbsolute(condaEnv))
-            cmd = "${binaryName} env create --prefix ${Escape.path(prefixPath)} --file ${target}"
+            final yesOpt = binaryName == 'micromamba' ? '--yes ' : ''
+            cmd = "${binaryName} env create ${yesOpt}--prefix ${Escape.path(prefixPath)} --file ${target}"
         }
         else if( isTextFilePath(condaEnv) ) {
             cmd = "${binaryName} create ${opts}--yes --quiet --prefix ${Escape.path(prefixPath)} --file ${Escape.path(makeAbsolute(condaEnv))}"
@@ -350,17 +360,18 @@ class CondaCache {
      */
     @PackageScope
     DataflowVariable<Path> getLazyImagePath(String condaEnv) {
-
-        if( condaEnv in condaPrefixPaths ) {
+        final prefixPath = condaPrefixPath(condaEnv)
+        final condaEnvPath = prefixPath.toString()
+        if( condaEnvPath in condaPrefixPaths ) {
             log.trace "${binaryName} found local environment `$condaEnv`"
-            return condaPrefixPaths[condaEnv]
+            return condaPrefixPaths[condaEnvPath]
         }
 
         synchronized (condaPrefixPaths) {
-            def result = condaPrefixPaths[condaEnv]
+            def result = condaPrefixPaths[condaEnvPath]
             if( result == null ) {
-                result = new LazyDataflowVariable<Path>({ createLocalCondaEnv(condaEnv) })
-                condaPrefixPaths[condaEnv] = result
+                result = new LazyDataflowVariable<Path>({ createLocalCondaEnv(condaEnv, prefixPath) })
+                condaPrefixPaths[condaEnvPath] = result
             }
             else {
                 log.trace "${binaryName} found local cache for environment `$condaEnv` (2)"
diff --git a/modules/nextflow/src/main/groovy/nextflow/config/ConfigBase.groovy b/modules/nextflow/src/main/groovy/nextflow/config/ConfigBase.groovy
index 46a6f182da..a97e23f19a 100644
--- a/modules/nextflow/src/main/groovy/nextflow/config/ConfigBase.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/config/ConfigBase.groovy
@@ -16,12 +16,12 @@
 
 package nextflow.config
 
-import ch.artecat.grengine.Grengine
-import groovy.transform.Memoized
-
 import java.nio.file.NoSuchFileException
 import java.nio.file.Path
 
+import ch.artecat.grengine.Grengine
+import groovy.transform.Memoized
+import nextflow.SysEnv
 import nextflow.exception.IllegalConfigException
 import nextflow.file.FileHelper
 import org.codehaus.groovy.control.CompilerConfiguration
@@ -74,6 +74,18 @@ abstract class ConfigBase extends Script {
         this.configStack = stack
     }
 
+    /**
+     * Get the value of an environment variable from the launch environment.
+     *
+     * @param name
+     *      The environment variable name to be referenced
+     * @return
+     *      The value associate with the specified variable name or {@code null} if the variable does not exist.
+     */
+    String env(String name) {
+        return SysEnv.get(name)
+    }
+
     /**
      * Implements the config file include
      */
diff --git a/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
index 08d5f3f011..841a1c9bcc 100644
--- a/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
@@ -545,6 +545,10 @@ class ConfigBuilder {
         if( cmdRun.stubRun )
             config.stubRun = cmdRun.stubRun
 
+        // -- set the output directory
+        if( cmdRun.outputDir )
+            config.outputDir = cmdRun.outputDir
+
         if( cmdRun.preview )
             config.preview = cmdRun.preview
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/config/ConfigClosurePlaceholder.groovy b/modules/nextflow/src/main/groovy/nextflow/config/ConfigClosurePlaceholder.groovy
index 2780ef34e3..1ceb074923 100644
--- a/modules/nextflow/src/main/groovy/nextflow/config/ConfigClosurePlaceholder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/config/ConfigClosurePlaceholder.groovy
@@ -18,8 +18,6 @@ package nextflow.config
 
 import groovy.transform.CompileStatic
 import groovy.transform.EqualsAndHashCode
-import groovy.transform.PackageScope
-
 /**
  * Placeholder class that replacing closure definitions in the nextflow configuration
  * file in order to print the closure content itself
@@ -28,7 +26,6 @@ import groovy.transform.PackageScope
  */
 @EqualsAndHashCode
 @CompileStatic
-@PackageScope
 class ConfigClosurePlaceholder {
 
     private String str
diff --git a/modules/nextflow/src/main/groovy/nextflow/config/Manifest.groovy b/modules/nextflow/src/main/groovy/nextflow/config/Manifest.groovy
index ad06fa0a49..626ce52e26 100644
--- a/modules/nextflow/src/main/groovy/nextflow/config/Manifest.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/config/Manifest.groovy
@@ -16,10 +16,13 @@
 
 package nextflow.config
 
+import java.util.stream.Collectors
 
 import groovy.transform.CompileStatic
+import groovy.transform.EqualsAndHashCode
 import groovy.util.logging.Slf4j
-import static nextflow.Const.DEFAULT_BRANCH
+import nextflow.exception.AbortOperationException
+
 import static nextflow.Const.DEFAULT_MAIN_FILE_NAME
 /**
  * Models the nextflow config manifest settings
@@ -52,7 +55,7 @@ class Manifest {
 
 
     String getDefaultBranch() {
-        target.defaultBranch ?: DEFAULT_BRANCH
+        target.defaultBranch
     }
 
     String getDescription() {
@@ -63,6 +66,21 @@ class Manifest {
         target.author
     }
 
+    List<Contributor> getContributors() {
+        if( !target.contributors )
+            return Collections.emptyList()
+
+        try {
+            final contributors = target.contributors as List<Map>
+            return contributors.stream()
+                .map(opts -> new Contributor(opts))
+                .collect(Collectors.toList())
+        }
+        catch( ClassCastException | IllegalArgumentException e ){
+            throw new AbortOperationException("Invalid config option `manifest.contributors` -- should be a list of maps")
+        }
+    }
+
     String getMainScript() {
         target.mainScript ?: DEFAULT_MAIN_FILE_NAME
     }
@@ -98,9 +116,28 @@ class Manifest {
         target.doi
     }
 
+    String getDocsUrl() {
+        target.docsUrl
+    }
+
+    String getIcon() {
+        target.icon
+    }
+
+    String getOrganization() {
+        target.organization
+    }
+
+    String getLicense() {
+        target.license
+    }
+
     Map toMap() {
-        final result = new HashMap(10)
+        final result = new HashMap(15)
         result.author = getAuthor()
+        result.contributors = getContributors().stream()
+            .map(c -> c.toMap())
+            .collect(Collectors.toList())
         result.defaultBranch = getDefaultBranch()
         result.description = getDescription()
         result.homePage = homePage
@@ -109,6 +146,51 @@ class Manifest {
         result.version = getVersion()
         result.nextflowVersion = getNextflowVersion()
         result.doi = getDoi()
+        result.docsUrl = getDocsUrl()
+        result.icon = getIcon()
+        result.organization = getOrganization()
+        result.license = getLicense()
         return result
     }
+
+    @EqualsAndHashCode
+    static class Contributor {
+        String name
+        String affiliation
+        String email
+        String github
+        Set<ContributionType> contribution
+        String orcid
+
+        Contributor(Map opts) {
+            name = opts.name as String
+            affiliation = opts.affiliation as String
+            email = opts.email as String
+            github = opts.github as String
+            contribution = (opts.contribution as List<String>).stream()
+                .map(c -> ContributionType.valueOf(c.toUpperCase()))
+                .collect(Collectors.toSet())
+            orcid = opts.orcid as String
+        }
+
+        Map toMap() {
+            final result = new HashMap(6)
+            result.name = name
+            result.affiliation = affiliation
+            result.email = email
+            result.github = github
+            result.contribution = contribution.stream()
+                .map(c -> c.toString().toLowerCase())
+                .sorted()
+                .collect(Collectors.toList())
+            result.orcid = orcid
+            return result
+        }
+    }
+
+    static enum ContributionType {
+        AUTHOR,
+        MAINTAINER,
+        CONTRIBUTOR
+    }
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/CharliecloudBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/container/CharliecloudBuilder.groovy
index 9a86e87e39..cd4f3f1eb5 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/CharliecloudBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/CharliecloudBuilder.groovy
@@ -19,6 +19,7 @@ import java.nio.file.Path
 import java.nio.file.Paths
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
+import nextflow.Global
 /**
  * Implements a builder for Charliecloud containerisation
  *
@@ -33,10 +34,8 @@ import groovy.util.logging.Slf4j
 @Slf4j
 class CharliecloudBuilder extends ContainerBuilder<CharliecloudBuilder> {
     
-    protected boolean useSquash
+    private boolean writeFake = true
 
-    protected boolean writeFake
-    
     CharliecloudBuilder(String name) {
         this.image = name
     }
@@ -52,16 +51,13 @@ class CharliecloudBuilder extends ContainerBuilder<CharliecloudBuilder> {
 
         if( params.containsKey('runOptions') )
             addRunOptions(params.runOptions.toString())
-
-        if ( params.containsKey('useSquash') )
-            this.useSquash = params.useSquash?.toString() == 'true'
-
+                
         if ( params.containsKey('writeFake') )
-            this.writeFake = params.writeFake?.toString() == 'true'
+            this.writeFake = params.writeFake?.toString() != 'false'
 
         if( params.containsKey('readOnlyInputs') )
             this.readOnlyInputs = params.readOnlyInputs?.toString() == 'true'
-
+        
         return this
     }
 
@@ -72,40 +68,22 @@ class CharliecloudBuilder extends ContainerBuilder<CharliecloudBuilder> {
 
     @Override
     CharliecloudBuilder build(StringBuilder result) {
+        
         assert image
         def imageStorage = Paths.get(image).parent.parent
-        def imageToRun = String
-
-        if (!writeFake) {
-            // define image to run, if --write-fake is not used this is a copy of the image in the current workDir
-            imageToRun = '"$NXF_TASK_WORKDIR"/container_' + image.split('/')[-1]
-
-            // optional squash
-            if (useSquash) {
-                imageToRun = imageToRun + '.squashfs'
-            }
-
-            result << 'ch-convert -i ch-image --storage '
-            // handle storage to deal with cases where CH_IMAGE_STORAGE is not set
-            result << imageStorage
-            result << ' '
-            result << image.split('/')[-1]
-            result << ' '
-            result << imageToRun
-            result << ' && '
-        }
+        def imageName = image.split('/')[-1]
 
         result << 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env '
-        
-        if (writeFake) {
-            result << '--write-fake ' 
-            // if we are using writeFake we do not need to create a temporary imagae
-            // image is run by name from the storage directory
-            imageToRun = image.split('/')[-1]
-        }
 
-        if (!readOnlyInputs)
+        if ( writeFake  )
+            result << '--write-fake '
+
+        if ( !writeFake && !readOnlyInputs ) {
+            // -w and CH_IMAGE_STORAGE are incompatible.
+            if(System.getenv('CH_IMAGE_STORAGE') == imageStorage)
+                throw new Exception('It is not possible to run writeable images from `$CH_IMAGE_STORAGE`')
             result << '-w '
+        }
 
         appendEnv(result)
 
@@ -116,8 +94,15 @@ class CharliecloudBuilder extends ContainerBuilder<CharliecloudBuilder> {
 
         if( runOptions )
             result << runOptions.join(' ') << ' '
+
+        if( writeFake && System.getenv('CH_IMAGE_STORAGE') ) {
+            // Run by name if writeFake is true and CH_IMAGE_STORAGE is set
+            result << imageName
+        } else {
+            // Otherwise run by path
+            result << image
+        }
         
-        result << imageToRun
         result << ' --'
 
         runCommand = result.toString()
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/CharliecloudCache.groovy b/modules/nextflow/src/main/groovy/nextflow/container/CharliecloudCache.groovy
index 0962477322..39ff86abb3 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/CharliecloudCache.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/CharliecloudCache.groovy
@@ -103,9 +103,10 @@ class CharliecloudCache {
     /**
      * Retrieve the directory where to store the charliecloud images once downloaded.
      * It tries these settings in the following order:
-     * 1) {@code charliecloud.cacheDir} setting in the nextflow config file
-     * 2) the {@code NXF_CHARLIECLOUD_CACHEDIR} environment variable
-     * 3) the {@code $workDir/charliecloud} path
+     * 1) If writeFake is enabled, the {@code CH_IMAGE_STORAGE} environment variable.
+     * 2) {@code charliecloud.cacheDir} setting in the nextflow config file
+     * 3) the {@code NXF_CHARLIECLOUD_CACHEDIR} environment variable
+     * 4) the {@code $workDir/charliecloud} path
      *
      * @return
      *      the {@code Path} where store the charliecloud images as flattened directories
@@ -116,19 +117,38 @@ class CharliecloudCache {
         if( config.pullTimeout )
             pullTimeout = config.pullTimeout as Duration
 
+        def writeFake = true
+
+        if( config.writeFake ) 
+            writeFake = config.writeFake?.toString() == 'true'
+
         def str = config.cacheDir as String
-        if( str )
+
+        def charliecloudImageStorage = env.get('CH_IMAGE_STORAGE')
+
+        if( charliecloudImageStorage && writeFake) {
+            return checkDir(charliecloudImageStorage)
+        }
+            
+        if( str ) {
+            // If charliecloudImageStorage exists and writeFake is true, we never get here
+            if( str.equals( charliecloudImageStorage ) ) {
+                throw new Exception("`charliecloud.cacheDir` configuration parameter must be different from env variable `CH_IMAGE_STORAGE`")
+            }
             return checkDir(str)
+        }
 
         str = env.get('NXF_CHARLIECLOUD_CACHEDIR')
-        if( str )
-            return checkDir(str)
 
-        str = env.get('CH_IMAGE_STORAGE')
-        if( str )
+        if( str ) {
+            if( str.equals( charliecloudImageStorage ) ) {
+                throw new Exception("`NXF_CHARLIECLOUD_CACHEDIR` env variable must be different from env variable `CH_IMAGE_STORAGE`")
+            }
             return checkDir(str)
+        }
 
         def workDir = Global.session.workDir
+
         if( workDir.fileSystem != FileSystems.default ) {
             throw new IOException("Charliecloud cannot store image in a remote work directory -- Use a POSIX compatible work directory or specify an alternative path with the `NXF_CHARLIECLOUD_CACHEDIR` env variable")
         }
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/inspect/ContainerInspectMode.groovy b/modules/nextflow/src/main/groovy/nextflow/container/inspect/ContainerInspectMode.groovy
index 4351b5ffea..4b3904e5db 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/inspect/ContainerInspectMode.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/inspect/ContainerInspectMode.groovy
@@ -26,10 +26,10 @@ import groovy.transform.CompileStatic
 @CompileStatic
 class ContainerInspectMode {
 
-    private static boolean active
+    private static Boolean active
 
-    static boolean active() { return active }
+    static boolean active() { return active==true }
 
-    static void activate(boolean value) { active=value }
+    static void activate(boolean value) { active = value }
 
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/inspect/ContainersInspector.groovy b/modules/nextflow/src/main/groovy/nextflow/container/inspect/ContainersInspector.groovy
index 1a2e6827f3..9a03dcee37 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/inspect/ContainersInspector.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/inspect/ContainersInspector.groovy
@@ -17,12 +17,16 @@
 
 package nextflow.container.inspect
 
+import java.util.concurrent.CompletableFuture
+import java.util.concurrent.Executors
+
 import groovy.json.JsonBuilder
 import groovy.json.JsonOutput
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.dag.DAG
 import nextflow.exception.AbortOperationException
+import nextflow.processor.TaskRun
 import org.codehaus.groovy.util.ListHashMap
 /**
  * Preview the list of containers used by a pipeline.
@@ -39,8 +43,11 @@ class ContainersInspector {
 
     private boolean ignoreErrors
 
-    ContainersInspector(DAG dag) {
+    private boolean concretize
+
+    ContainersInspector(DAG dag, boolean concretize) {
         this.dag = dag
+        this.concretize = concretize
     }
 
     ContainersInspector withFormat(String format) {
@@ -75,6 +82,7 @@ class ContainersInspector {
     protected Map<String,String> getContainers() {
         final containers = new ListHashMap<String,String>()
 
+        List<TaskRun> tasks = new ArrayList<>()
         for( def vertex : dag.vertices ) {
             // skip nodes that are not processes
             final process = vertex.process
@@ -83,7 +91,11 @@ class ContainersInspector {
 
             try {
                 // get container preview
-                containers[process.name] = process.createTaskPreview().getContainer()
+                final task = process.createTaskPreview()
+                final containerName = task.getContainer()
+                containers[process.name] = containerName
+                if( containerName )
+                    tasks.add(task)
             }
             catch( Exception e ) {
                 if( ignoreErrors )
@@ -92,10 +104,42 @@ class ContainersInspector {
                     throw e
             }
         }
-
+        // await for containers to be
+        if( concretize ) {
+            await(tasks)
+        }
         return containers
     }
 
+    protected void await(List<TaskRun> tasks) {
+        if( !tasks )
+            return
+        final executor = Executors.newFixedThreadPool(10)
+        CompletableFuture<Void>[] futures = new CompletableFuture<Void>[tasks.size()]
+        for( int i=0; i<tasks.size(); i++ ) {
+            final t = tasks[i]
+            futures[i] = CompletableFuture.runAsync(() -> {
+                try {
+                    int c=0
+                    while( !t.isContainerReady() ) {
+                        Thread.sleep(c++< 10 ? 1_000 : 5_000)
+                    }
+                }
+                catch (InterruptedException e) {
+                    Thread.currentThread().interrupt();
+                }
+            }, executor)
+        }
+
+        // Wait for all tasks to complete
+        CompletableFuture<Void> allFutures = CompletableFuture.allOf(futures)
+
+        // Block until all tasks are completed
+        allFutures.join();  // This will wait until all tasks complete
+        // Shut down the executor
+        executor.shutdown()
+    }
+
     protected String renderConfig(Map<String,String> containers) {
         final result = new StringBuilder()
         for( Map.Entry<String,String> entry : containers ) {
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/resolver/ContainerResolver.groovy b/modules/nextflow/src/main/groovy/nextflow/container/resolver/ContainerResolver.groovy
index 4ccd19c2a1..ec2cf3302c 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/resolver/ContainerResolver.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/resolver/ContainerResolver.groovy
@@ -44,6 +44,14 @@ interface ContainerResolver extends ExtensionPoint {
      * @return
      *      The resolved container image name
      */
-    abstract ContainerInfo resolveImage(TaskRun task, String imageName)
+    ContainerInfo resolveImage(TaskRun task, String imageName)
+
+    /**
+     * Check the availability of the specified container reference
+     *
+     * @param key The container reference
+     * @return {@code true} when the container is available for use, {@code false} otherwise
+     */
+    boolean isContainerReady(String key)
 
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/resolver/DefaultContainerResolver.groovy b/modules/nextflow/src/main/groovy/nextflow/container/resolver/DefaultContainerResolver.groovy
index 8e83ccbd32..203a42431d 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/resolver/DefaultContainerResolver.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/resolver/DefaultContainerResolver.groovy
@@ -55,4 +55,8 @@ class DefaultContainerResolver implements ContainerResolver {
         return new ContainerInfo(imageName, ret, hashKey)
     }
 
+    @Override
+    boolean isContainerReady(String key) {
+        return true
+    }
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/datasource/SraExplorer.groovy b/modules/nextflow/src/main/groovy/nextflow/datasource/SraExplorer.groovy
index 8c0f118beb..c1d01f1d2e 100644
--- a/modules/nextflow/src/main/groovy/nextflow/datasource/SraExplorer.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/datasource/SraExplorer.groovy
@@ -16,6 +16,12 @@
 
 package nextflow.datasource
 
+import dev.failsafe.Failsafe
+import dev.failsafe.RetryPolicy
+import dev.failsafe.event.EventListener
+import dev.failsafe.event.ExecutionAttemptedEvent
+import dev.failsafe.function.CheckedSupplier
+
 import java.nio.file.NoSuchFileException
 import java.nio.file.Path
 
@@ -34,6 +40,11 @@ import nextflow.extension.FilesEx
 import nextflow.file.FileHelper
 import nextflow.util.CacheHelper
 import nextflow.util.Duration
+
+import java.time.temporal.ChronoUnit
+import java.util.function.Predicate
+import java.util.regex.Pattern
+
 /**
  * Query NCBI SRA database and returns the retrieved FASTQs to the specified
  * target channel. Inspired to SRA-Explorer by Phil Ewels -- https://ewels.github.io/sra-explorer/
@@ -43,7 +54,9 @@ import nextflow.util.Duration
 @Slf4j
 class SraExplorer {
 
-    static public Map PARAMS = [apiKey:[String,GString], cache: Boolean, max: Integer, protocol: ['ftp','http','https']]
+    static public Map PARAMS = [apiKey:[String,GString], cache: Boolean, max: Integer, protocol: ['ftp','http','https'], retryPolicy: Map]
+    final static public List<Integer> RETRY_CODES = List.of(408, 429, 500, 502, 503, 504)
+    final static private Pattern ERROR_PATTERN = ~/Server returned HTTP response code: (\d+) for URL.*/
 
     @ToString
     static class SearchRecord {
@@ -67,6 +80,7 @@ class SraExplorer {
     private List<String> missing = new ArrayList<>()
     private Path cacheFolder
     private String protocol = 'ftp'
+    private SraRetryConfig retryConfig = new SraRetryConfig()
 
     String apiKey
     boolean useCache = true
@@ -94,6 +108,8 @@ class SraExplorer {
             maxResults = opts.max as int
         if( opts.protocol )
             protocol = opts.protocol as String
+        if( opts.retryPolicy )
+            retryConfig = new SraRetryConfig(opts.retryPolicy as Map)
     }
 
     DataflowWriteChannel apply() {
@@ -181,7 +197,7 @@ class SraExplorer {
 
     protected Map makeDataRequest(String url) {
         log.debug "SRA data request url=$url"
-        final text = new URL(url).getText()
+        final text = runWithRetry(()->getTextFormUrl(url))
 
         log.trace "SRA data result:\n${pretty(text)?.indent()}"
         def response = jsonSlurper.parseText(text)
@@ -220,7 +236,7 @@ class SraExplorer {
 
     protected SearchRecord makeSearch(String url) {
         log.debug "SRA search url=$url"
-        final text = new URL(url).getText()
+        final text = runWithRetry(()-> getTextFormUrl(url))
 
         log.trace "SRA search result:\n${pretty(text)?.indent()}"
         final response = jsonSlurper.parseText(text)
@@ -265,10 +281,14 @@ class SraExplorer {
         return result
     }
 
+    protected static String getTextFormUrl(String url) {
+        new URI(url).toURL().getText()
+    }
+
     protected String readRunUrl(String acc) {
         final url = "https://www.ebi.ac.uk/ena/portal/api/filereport?result=read_run&fields=fastq_ftp&accession=$acc"
         log.debug "SRA fetch ftp fastq url=$url"
-        String result = new URL(url).text.trim()
+        String result = runWithRetry(() -> getTextFormUrl(url)).trim()
         log.trace "SRA fetch ftp fastq url result:\n${result?.indent()}"
 
         if( result.indexOf('\n')==-1 ) {
@@ -330,6 +350,66 @@ class SraExplorer {
         return url
     }
 
+    /**
+     * Creates a retry policy using the SRA retry configuration
+     *
+     * @param cond A predicate that determines when a retry should be triggered
+     * @return The {@link dev.failsafe.RetryPolicy} instance
+     */
+    protected <T> RetryPolicy<T> retryPolicy(Predicate<? extends Throwable> cond) {
+        final EventListener<ExecutionAttemptedEvent> listener = new EventListener<ExecutionAttemptedEvent>() {
+            @Override
+            void accept(ExecutionAttemptedEvent event) throws Throwable {
+                log.debug("Retryable response error - attempt: ${event.attemptCount}; reason: ${event.lastFailure.message}")
+            }
+        }
+        return RetryPolicy.<T>builder()
+            .handleIf(cond)
+            .withBackoff(retryConfig.delay.toMillis(), retryConfig.maxDelay.toMillis(), ChronoUnit.MILLIS)
+            .withMaxAttempts(retryConfig.maxAttempts)
+            .withJitter(retryConfig.jitter)
+            .onRetry(listener)
+            .build()
+    }
+
+    /**
+     * Carry out the invocation of the specified action using a retry policy
+     * when {@link java.io.IOException} is returned containing an error code.
+     *
+     * @param action A {@link dev.failsafe.function.CheckedSupplier} instance modeling the action to be performed in a safe manner
+     * @return The result of the supplied action
+     */
+    protected <T> T runWithRetry(CheckedSupplier<T> action) {
+        // define listener
+        final listener = new EventListener<ExecutionAttemptedEvent>() {
+            @Override
+            void accept(ExecutionAttemptedEvent event) throws Throwable {
+                log.debug("Retryable response error - attempt: ${event.attemptCount}; reason: ${event.lastFailure.message}")
+            }
+        }
+        // define the retry condition
+        final cond = new Predicate<? extends Throwable>() {
+            @Override
+            boolean test(Throwable t) {
+                if( t instanceof IOException && containsErrorCodes(t.message, RETRY_CODES))
+                    return true
+                if(t.cause instanceof IOException && containsErrorCodes(t.cause.message, RETRY_CODES))
+                    return true
+                return false
+            }
+        }
+        // create the retry policy
+        def policy = retryPolicy(cond)
+        // apply the action with
+        return Failsafe.with(policy).get(action)
+    }
+
+    static boolean containsErrorCodes(String message, List<Integer> codes){
+        def matcher = (message =~ ERROR_PATTERN)
+        def httpCode = matcher ? matcher[0][1] as Integer : null
+        return httpCode != null && codes.contains(httpCode)
+    }
+
 }
 
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/datasource/SraRetryConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/datasource/SraRetryConfig.groovy
new file mode 100644
index 0000000000..f752a54a3d
--- /dev/null
+++ b/modules/nextflow/src/main/groovy/nextflow/datasource/SraRetryConfig.groovy
@@ -0,0 +1,52 @@
+/*
+ * Copyright 2013-2024, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.datasource
+
+import groovy.transform.CompileStatic
+import groovy.transform.EqualsAndHashCode
+import groovy.transform.ToString
+import nextflow.util.Duration
+/**
+ * Models retry policy configuration for Sra queries
+ *
+ * @author Jorge Ejarque <jorge.ejarque@seqera.io>
+ */
+@ToString(includePackage = false, includeNames = true)
+@EqualsAndHashCode
+@CompileStatic
+class SraRetryConfig {
+    Duration delay = Duration.of('500ms')
+    Duration maxDelay = Duration.of('30s')
+    int maxAttempts = 3
+    double jitter = 0.25
+
+    SraRetryConfig() {
+        this(Collections.emptyMap())
+    }
+
+    SraRetryConfig(Map config) {
+        if( config.delay )
+            delay = config.delay as Duration
+        if( config.maxDelay )
+            maxDelay = config.maxDelay as Duration
+        if( config.maxAttempts )
+            maxAttempts = config.maxAttempts as int
+        if( config.jitter )
+            jitter = config.jitter as double
+    }
+}
diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/AbstractGridExecutor.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/AbstractGridExecutor.groovy
index 6d6b7cc0a4..306352bbb8 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/AbstractGridExecutor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/AbstractGridExecutor.groovy
@@ -41,7 +41,7 @@ abstract class AbstractGridExecutor extends Executor {
 
     protected Duration queueInterval
 
-    private final static List<String> INVALID_NAME_CHARS = [ " ", "/", ":", "@", "*", "?", "\\n", "\\t", "\\r" ]
+    private final static List<String> INVALID_NAME_CHARS = [ " ", "/", ":", "@", "*", "?", "\\n", "\\t", "\\r", "=" ]
 
     private Map lastQueueStatus
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
index 5efb06dcf3..0b0fac4a81 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
@@ -534,10 +534,13 @@ class BashWrapperBuilder {
     private String getCondaActivateSnippet() {
         if( !condaEnv )
             return null
-        def result = "# conda environment\n"
-        result += 'source $(conda info --json | awk \'/conda_prefix/ { gsub(/"|,/, "", $2); print $2 }\')'
-        result += "/bin/activate ${Escape.path(condaEnv)}\n"
-        return result
+        final command = useMicromamba
+            ? 'eval "$(micromamba shell hook --shell bash)" && micromamba activate'
+            : 'source $(conda info --json | awk \'/conda_prefix/ { gsub(/"|,/, "", $2); print $2 }\')/bin/activate'
+        return """\
+            # conda environment
+            ${command} ${Escape.path(condaEnv)}
+            """.stripIndent()
     }
 
     private String getSpackActivateSnippet() {
@@ -758,7 +761,7 @@ class BashWrapperBuilder {
         result += copyFileToWorkDir(TaskRun.CMD_ERRFILE) + ' || true' + ENDL
         if( statsEnabled )
             result += copyFileToWorkDir(TaskRun.CMD_TRACE) + ' || true' + ENDL
-        if(  outputEnvNames )
+        if( outputEnvNames || outputEvals )
             result += copyFileToWorkDir(TaskRun.CMD_ENV) + ' || true' + ENDL
         return result
     }
diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/Executor.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/Executor.groovy
index 1d6d92f37e..4af74bfe1f 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/Executor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/Executor.groovy
@@ -93,7 +93,7 @@ abstract class Executor {
         /*
          * Add the task to the queue for processing
          * Note: queue is implemented as a fixed size blocking queue, when
-         * there's not space *put* operation will block until, some other tasks finish
+         * there's not space the *put* operation will block until some other tasks finish
          */
         monitor.schedule(handler)
     }
diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/FluxExecutor.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/FluxExecutor.groovy
index 25d96fc78e..b6184dde07 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/FluxExecutor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/FluxExecutor.groovy
@@ -61,7 +61,7 @@ class FluxExecutor extends AbstractGridExecutor {
     @Override
     List<String> getSubmitCommandLine(TaskRun task, Path scriptFile ) {
 
-        List<String> result = ['flux', 'mini', 'submit']
+        List<String> result = ['flux', 'submit']
         result << '--setattr=cwd=' + quote(task.workDir)
         result << '--job-name="' + getJobNameFor(task) + '"'
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/PbsExecutor.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/PbsExecutor.groovy
index 8e968f99c7..b25f020648 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/PbsExecutor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/PbsExecutor.groovy
@@ -46,7 +46,7 @@ class PbsExecutor extends AbstractGridExecutor implements TaskArrayExecutor {
 
         if( task instanceof TaskArrayRun ) {
             final arraySize = task.getArraySize()
-            result << '-J' << "0-${arraySize - 1}".toString()
+            result << '-t' << "0-${arraySize - 1}".toString()
         }
 
         result << '-N' << getJobNameFor(task)
@@ -188,7 +188,7 @@ class PbsExecutor extends AbstractGridExecutor implements TaskArrayExecutor {
 
     @Override
     String getArrayIndexName() {
-        return 'PBS_ARRAY_INDEX'
+        return 'PBS_ARRAYID'
     }
 
     @Override
diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/PbsProExecutor.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/PbsProExecutor.groovy
index c171657224..bcb0cbfa84 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/PbsProExecutor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/PbsProExecutor.groovy
@@ -129,4 +129,9 @@ class PbsProExecutor extends PbsExecutor {
         DECODE_STATUS.get(status)
     }
 
+    @Override
+    String getArrayIndexName() {
+        return 'PBS_ARRAY_INDEX'
+    }
+
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/SimpleFileCopyStrategy.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/SimpleFileCopyStrategy.groovy
index e1a92b172c..6d9dcbd538 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/SimpleFileCopyStrategy.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/SimpleFileCopyStrategy.groovy
@@ -183,7 +183,7 @@ class SimpleFileCopyStrategy implements ScriptFileCopyStrategy {
         return """\
             IFS=\$'\\n'
             for name in \$(eval "ls -1d ${escape.join(' ')}" | sort | uniq); do
-                ${stageOutCommand('$name', targetDir, mode)} || true
+                ${stageOutCommand('$name', targetDir, mode)}
             done
             unset IFS""".stripIndent(true)
     }
diff --git a/modules/nextflow/src/main/groovy/nextflow/extension/PublishOp.groovy b/modules/nextflow/src/main/groovy/nextflow/extension/PublishOp.groovy
index 12f2e9d896..3f10b7c16c 100644
--- a/modules/nextflow/src/main/groovy/nextflow/extension/PublishOp.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/extension/PublishOp.groovy
@@ -18,6 +18,7 @@ package nextflow.extension
 
 import java.nio.file.Path
 
+import groovy.json.JsonOutput
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import groovyx.gpars.dataflow.DataflowReadChannel
@@ -36,10 +37,12 @@ class PublishOp {
 
     private DataflowReadChannel source
 
-    private PublishDir publisher
+    private Map opts
 
     private Path targetDir
 
+    private Closure pathAs
+
     private IndexOpts indexOpts
 
     private List indexRecords = []
@@ -50,8 +53,10 @@ class PublishOp {
 
     PublishOp(DataflowReadChannel source, Map opts) {
         this.source = source
-        this.publisher = PublishDir.create(opts)
+        this.opts = opts
         this.targetDir = opts.path as Path
+        if( opts.pathAs instanceof Closure )
+            this.pathAs = opts.pathAs as Closure
         if( opts.index )
             this.indexOpts = new IndexOpts(targetDir, opts.index as Map)
     }
@@ -68,6 +73,24 @@ class PublishOp {
 
     protected void onNext(value) {
         log.trace "Publish operator received: $value"
+
+        // evaluate dynamic path
+        final path = pathAs != null
+            ? pathAs.call(value)
+            : targetDir
+        if( path == null )
+            return
+
+        // emit workflow publish event
+        session.notifyWorkflowPublish(value)
+
+        // create publisher
+        final overrides = path instanceof Closure
+            ? [saveAs: path]
+            : [path: path]
+        final publisher = PublishDir.create(opts + overrides)
+
+        // publish files
         final result = collectFiles([:], value)
         for( final entry : result ) {
             final sourceDir = entry.key
@@ -75,6 +98,7 @@ class PublishOp {
             publisher.apply(files, sourceDir)
         }
 
+        // create record for index file
         if( indexOpts ) {
             final record = indexOpts.mapper != null ? indexOpts.mapper.call(value) : value
             final normalized = normalizePaths(record)
@@ -84,9 +108,15 @@ class PublishOp {
     }
 
     protected void onComplete(nope) {
-        if( indexOpts && indexRecords.size() > 0 && publisher.enabled ) {
+        if( indexOpts && indexRecords.size() > 0 ) {
             log.trace "Saving records to index file: ${indexRecords}"
-            new CsvWriter(header: indexOpts.header, sep: indexOpts.sep).apply(indexRecords, indexOpts.path)
+            final ext = indexOpts.path.getExtension()
+            if( ext == 'csv' )
+                new CsvWriter(header: indexOpts.header, sep: indexOpts.sep).apply(indexRecords, indexOpts.path)
+            else if( ext == 'json' )
+                indexOpts.path.text = DumpHelper.prettyPrint(indexRecords)
+            else
+                log.warn "Invalid extension '${ext}' for index file '${indexOpts.path}' -- should be 'csv' or 'json'"
             session.notifyFilePublish(indexOpts.path)
         }
 
@@ -150,7 +180,7 @@ class PublishOp {
 
     private Path normalizePath(Path path) {
         final sourceDir = getTaskDir(path)
-        return targetDir.resolve(sourceDir.relativize(path))
+        return targetDir.resolve(sourceDir.relativize(path)).normalize()
     }
 
     /**
diff --git a/modules/nextflow/src/main/groovy/nextflow/file/FilePorter.groovy b/modules/nextflow/src/main/groovy/nextflow/file/FilePorter.groovy
index 881f7ff6a4..6b138fe8aa 100644
--- a/modules/nextflow/src/main/groovy/nextflow/file/FilePorter.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/file/FilePorter.groovy
@@ -305,6 +305,15 @@ class FilePorter {
             }
         }
 
+        protected void cleanup(Path path) {
+            try {
+                FileHelper.deletePath(path)
+            }
+            catch (IOException e) {
+                log.warn "Unable to cleanup file path: ${path.toUriString()} - cause: ${e.message}"
+            }
+        }
+
         /**
          * Download a foreign file (ie. remote) storing it the current pipeline execution directory
          *
@@ -319,8 +328,11 @@ class FilePorter {
                     return stageForeignFile0(filePath, stagePath)
                 }
                 catch( IOException e ) {
+                    // remove the target file that could be have partially downloaded
+                    cleanup(stagePath)
+                    // check if a stage/download retry is allowed
                     if( count++ < maxRetries && e !instanceof NoSuchFileException && e !instanceof InterruptedIOException && !Thread.currentThread().isInterrupted() ) {
-                        def message = "Unable to stage foreign file: ${filePath.toUriString()} (try ${count}) -- Cause: $e.message"
+                        def message = "Unable to stage foreign file: ${filePath.toUriString()} (try ${count} of ${maxRetries}) -- Cause: $e.message"
                         log.isDebugEnabled() ? log.warn(message, e) : log.warn(message)
 
                         sleep (10 + RND.nextInt(300))
diff --git a/modules/nextflow/src/main/groovy/nextflow/k8s/client/K8sClient.groovy b/modules/nextflow/src/main/groovy/nextflow/k8s/client/K8sClient.groovy
index 6fe1f75a19..ea9193be3f 100644
--- a/modules/nextflow/src/main/groovy/nextflow/k8s/client/K8sClient.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/k8s/client/K8sClient.groovy
@@ -487,7 +487,7 @@ class K8sClient {
             if( status.conditions instanceof List ) {
                 final allConditions = status.conditions as List<Map>
                 final cond = allConditions.find { cond -> cond.type == 'PodScheduled' }
-                if( cond.reason == 'Unschedulable' ) {
+                if( cond?.reason == 'Unschedulable' ) {
                     def message = "K8s pod cannot be scheduled"
                     if( cond.message ) message += " -- $cond.message"
                     //def cause = new K8sResponseException(resp)
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy
index ee2a5342ee..4ca5764519 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy
@@ -219,11 +219,19 @@ class PublishDir {
         return result
     }
 
+    protected Map getRetryOpts() {
+        def result = session.config.navigate('nextflow.publish.retryPolicy') as Map
+        if( result != null )
+            log.warn 'The `nextflow.publish` config scope has been renamed to `workflow.output`'
+        else
+            result = session.config.navigate('workflow.output.retryPolicy') as Map ?: Collections.emptyMap()
+        return result
+    }
+
     protected void apply0(Set<Path> files) {
         assert path
-
-        final retryOpts = session.config.navigate('nextflow.publish.retryPolicy') as Map ?: Collections.emptyMap()
-        this.retryConfig = new PublishRetryConfig(retryOpts)
+        // setup the retry policy config to be used
+        this.retryConfig = new PublishRetryConfig(getRetryOpts())
 
         createPublishDir()
         validatePublishMode()
@@ -317,7 +325,7 @@ class PublishDir {
             return
         }
 
-        final destination = resolveDestination(target)
+        final destination = resolveDestination(target).normalize()
 
         // apply tags
         if( this.tags!=null && destination instanceof TagAwareFile ) {
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskBean.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskBean.groovy
index d1be0cf236..5d4175aeff 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskBean.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskBean.groovy
@@ -48,6 +48,8 @@ class TaskBean implements Serializable, Cloneable {
 
     Path condaEnv
 
+    Boolean useMicromamba
+
     Path spackEnv
 
     List<String> moduleNames
@@ -131,6 +133,7 @@ class TaskBean implements Serializable, Cloneable {
         this.environment = task.getEnvironment()
 
         this.condaEnv = task.getCondaEnv()
+        this.useMicromamba = task.getCondaConfig()?.useMicromamba()
         this.spackEnv = task.getSpackEnv()
         this.moduleNames = task.config.getModule()
         this.shell = task.config.getShell() ?: BashWrapperBuilder.BASH
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskConfig.groovy
index 3dcac1d3e8..cb78900b33 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskConfig.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskConfig.groovy
@@ -103,7 +103,7 @@ class TaskConfig extends LazyMap implements Cloneable {
         return eval0(this, path.tokenize('.'), path)
     }
 
-    private Object eval0(Object object, List<String> path, String key ) {
+    private Object eval0(Object object, List<String> path, String key) {
         assert path, "Missing task attribute name"
         def result = null
         if( object instanceof LazyMap ) {
@@ -345,8 +345,7 @@ class TaskConfig extends LazyMap implements Cloneable {
 
     int getMaxRetries() {
         def result = get('maxRetries')
-        def defResult = getErrorStrategy() == ErrorStrategy.RETRY ? 1 : 0
-        result ? result as int : defResult
+        result ? result as int : 1
     }
 
     int getMaxErrors() {
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskHandler.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskHandler.groovy
index e39a2a86da..80eb0289d3 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskHandler.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskHandler.groovy
@@ -243,6 +243,16 @@ abstract class TaskHandler {
         return !max ? true : task.processor.forksCount < max
     }
 
+    /**
+     * Determine if a task is ready for execution or it depends on resources
+     * e.g. container that needs to be provisionied
+     *
+     * @return {@code true} when the task is ready for execution, {@code false} otherwise
+     */
+    boolean isReady() {
+        task.isContainerReady()
+    }
+
     /**
      * Increment the number of current forked processes
      */
@@ -274,4 +284,21 @@ abstract class TaskHandler {
             return true
         return false
     }
+
+    /**
+     * Prepend the workflow Id to the job/task name. The workflow id is defined
+     * by the environment variable {@code TOWER_WORKFLOW_ID}
+     *
+     * @param name
+     *      The desired job name
+     * @param env
+     *      A map representing the variables in the host environment
+     * @return
+     *  The job having the prefix {@code tw-<ID>} when the variable {@code TOWER_WORKFLOW_ID}
+     *  is defined in the host environment or just {@code name} otherwise
+     */
+    static String prependWorkflowPrefix(String name, Map<String,String> env) {
+        final workflowId = env.get("TOWER_WORKFLOW_ID")
+        return workflowId ? "tw-${workflowId}-${name}" : name
+    }
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskPollingMonitor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskPollingMonitor.groovy
index 29a820624e..4e97543d2e 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskPollingMonitor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskPollingMonitor.groovy
@@ -16,6 +16,8 @@
 
 package nextflow.processor
 
+import static nextflow.processor.TaskProcessor.*
+
 import java.util.concurrent.ExecutorService
 import java.util.concurrent.LinkedBlockingQueue
 import java.util.concurrent.TimeUnit
@@ -191,7 +193,7 @@ class TaskPollingMonitor implements TaskMonitor {
      *      by the polling monitor
      */
     protected boolean canSubmit(TaskHandler handler) {
-        (capacity>0 ? runningQueue.size() < capacity : true) && handler.canForkProcess()
+        (capacity>0 ? runningQueue.size() < capacity : true) && handler.canForkProcess() && handler.isReady()
     }
 
     /**
@@ -587,7 +589,7 @@ class TaskPollingMonitor implements TaskMonitor {
 
         int count = 0
         def itr = pendingQueue.iterator()
-        while( itr.hasNext() && session.isSuccess() ) {
+        while( itr.hasNext() && session.canSubmitTasks() ) {
             final handler = itr.next()
             submitRateLimit?.acquire()
             try {
@@ -617,7 +619,7 @@ class TaskPollingMonitor implements TaskMonitor {
             if (evict(handler)) { 
                 handler.decProcessForks()
             }
-            fault = handler.task.processor.resumeOrDie(handler?.task, error)
+            fault = handler.task.processor.resumeOrDie(handler?.task, error, handler.getTraceRecord())
             log.trace "Task fault (1): $fault"
         }
         finally {
@@ -683,7 +685,7 @@ class TaskPollingMonitor implements TaskMonitor {
 
     protected void finalizeTask( TaskHandler handler ) {
         // finalize the task execution
-        final fault = handler.task.processor.finalizeTask(handler.task)
+        final fault = handler.task.processor.finalizeTask(handler)
 
         // notify task completion
         session.notifyTaskComplete(handler)
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index 7c9076d826..10205abbec 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -15,6 +15,8 @@
  */
 package nextflow.processor
 
+import nextflow.trace.TraceRecord
+
 import static nextflow.processor.ErrorStrategy.*
 
 import java.lang.reflect.InvocationTargetException
@@ -85,7 +87,6 @@ import nextflow.script.BodyDef
 import nextflow.script.ProcessConfig
 import nextflow.script.ScriptMeta
 import nextflow.script.ScriptType
-import nextflow.script.TaskClosure
 import nextflow.script.bundle.ResourcesBundle
 import nextflow.script.params.BaseOutParam
 import nextflow.script.params.CmdEvalParam
@@ -308,6 +309,8 @@ class TaskProcessor {
         this.ownerScript = script
         this.config = config
         this.taskBody = taskBody
+        if( taskBody.isShell )
+            log.warn "Process ${name} > the `shell` block is deprecated, use `script` instead"
         this.name = name
         this.maxForks = config.maxForks && config.maxForks>0 ? config.maxForks as int : 0
         this.forksCount = maxForks ? new LongAdder() : null
@@ -642,14 +645,8 @@ class TaskProcessor {
         if( !checkWhenGuard(task) )
             return
 
-        TaskClosure block
-        if( session.stubRun && (block=task.config.getStubBlock()) ) {
-            task.resolve(block)
-        }
-        else {
-            // -- resolve the task command script
-            task.resolve(taskBody)
-        }
+        // -- resolve the task command script
+        task.resolve(taskBody)
 
         // -- verify if exists a stored result for this case,
         //    if true skip the execution and return the stored data
@@ -1023,7 +1020,7 @@ class TaskProcessor {
      *      a {@link ErrorStrategy#TERMINATE})
      */
     @PackageScope
-    final synchronized resumeOrDie( TaskRun task, Throwable error ) {
+    final synchronized resumeOrDie( TaskRun task, Throwable error, TraceRecord traceRecord = null) {
         log.debug "Handling unexpected condition for\n  task: name=${safeTaskName(task)}; work-dir=${task?.workDirStr}\n  error [${error?.class?.name}]: ${error?.getMessage()?:error}"
 
         ErrorStrategy errorStrategy = TERMINATE
@@ -1068,6 +1065,10 @@ class TaskProcessor {
                 task.config.exitStatus = task.exitStatus
                 task.config.errorCount = procErrCount
                 task.config.retryCount = taskErrCount
+                //Add trace of the previous execution in the task context for next execution
+                if ( traceRecord )
+                    task.config.previousTrace = traceRecord
+                task.config.previousException = error
 
                 errorStrategy = checkErrorStrategy(task, error, taskErrCount, procErrCount, submitRetries)
                 if( errorStrategy.soft ) {
@@ -1285,6 +1286,9 @@ class TaskProcessor {
         if( task?.workDir )
             message << "\nWork dir:\n  ${task.workDirStr}"
 
+        if( task?.isContainerEnabled() )
+            message << "\nContainer:\n  ${task.container}".toString()
+
         message << suggestTip(message)
 
         return message
@@ -2365,7 +2369,8 @@ class TaskProcessor {
      * @param task The {@code TaskRun} instance to finalize
      */
     @PackageScope
-    final finalizeTask( TaskRun task ) {
+    final finalizeTask( TaskHandler handler) {
+        def task = handler.task
         log.trace "finalizing process > ${safeTaskName(task)} -- $task"
 
         def fault = null
@@ -2388,7 +2393,7 @@ class TaskProcessor {
             collectOutputs(task)
         }
         catch ( Throwable error ) {
-            fault = resumeOrDie(task, error)
+            fault = resumeOrDie(task, error, handler.getTraceRecord())
             log.trace "Task fault (3): $fault"
         }
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy
index 52670a3a1e..38b4ba4782 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy
@@ -16,6 +16,8 @@
 
 package nextflow.processor
 
+import nextflow.conda.CondaConfig
+
 import java.nio.file.FileSystems
 import java.nio.file.NoSuchFileException
 import java.nio.file.Path
@@ -23,12 +25,13 @@ import java.util.concurrent.ConcurrentHashMap
 import java.util.function.Function
 
 import com.google.common.hash.HashCode
-import groovy.transform.PackageScope
+import groovy.transform.Memoized
 import groovy.util.logging.Slf4j
 import nextflow.Session
 import nextflow.conda.CondaCache
 import nextflow.container.ContainerConfig
 import nextflow.container.resolver.ContainerInfo
+import nextflow.container.resolver.ContainerResolver
 import nextflow.container.resolver.ContainerResolverProvider
 import nextflow.exception.ProcessException
 import nextflow.exception.ProcessTemplateException
@@ -326,6 +329,11 @@ class TaskRun implements Cloneable {
      */
     volatile ErrorStrategy errorAction
 
+    /**
+     * Unique key for the container used by this task
+     */
+    volatile String containerKey
+
     TaskConfig config
 
     TaskContext context
@@ -671,6 +679,11 @@ class TaskRun implements Cloneable {
             }})
     }
 
+    @Memoized
+    private ContainerResolver containerResolver() {
+        ContainerResolverProvider.load()
+    }
+
     private ContainerInfo containerInfo0() {
         // fetch the container image from the config
         def configImage = config.getContainer()
@@ -681,8 +694,11 @@ class TaskRun implements Cloneable {
         if( !configImage )
             configImage = null
 
-        final res = ContainerResolverProvider.load()
-        final info = res.resolveImage(this, configImage as String)
+        final info = containerResolver().resolveImage(this, configImage as String)
+        // track the key of the container used
+        if( info!=null )
+            this.containerKey = info.hashKey
+        // return the info
         return info
     }
 
@@ -699,6 +715,12 @@ class TaskRun implements Cloneable {
         return info?.hashKey
     }
 
+    boolean isContainerReady() {
+       return containerKey
+            ? containerResolver().isContainerReady(containerKey)
+            : true
+    }
+
     ResourcesBundle getModuleBundle() {
         return this.getProcessor().getModuleBundle()
     }
@@ -767,7 +789,13 @@ class TaskRun implements Cloneable {
      *
      * @param body A {@code BodyDef} object instance
      */
-    @PackageScope void resolve(BodyDef body) {
+    void resolve(BodyDef body)  {
+        processor.session.stubRun && config.getStubBlock()
+            ? resolveStub(config.getStubBlock())
+            : resolveBody(body)
+    }
+
+    protected void resolveBody(BodyDef body) {
 
         // -- initialize the task code to be executed
         this.code = body.closure.clone() as Closure
@@ -809,7 +837,7 @@ class TaskRun implements Cloneable {
             throw new ProcessUnrecoverableException("Process `${getName()}` script is empty")
     }
 
-    @PackageScope void resolve(TaskClosure block) {
+    protected void resolveStub(TaskClosure block) {
         this.code = block.clone() as Closure
         this.code.delegate = this.context
         this.code.setResolveStrategy(Closure.DELEGATE_ONLY)
@@ -941,5 +969,9 @@ class TaskRun implements Cloneable {
     TaskBean toTaskBean() {
         return new TaskBean(this)
     }
+
+    CondaConfig getCondaConfig() {
+        return processor.session.getCondaConfig()
+    }
 }
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy b/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy
index dd304ad59e..a1b7d57683 100644
--- a/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy
@@ -55,6 +55,8 @@ import org.eclipse.jgit.merge.MergeStrategy
 @Slf4j
 @CompileStatic
 class AssetManager {
+    private static final String REMOTE_REFS_ROOT = "refs/remotes/origin/"
+    private static final String REMOTE_DEFAULT_HEAD = REMOTE_REFS_ROOT + "HEAD"
 
     /**
      * The folder all pipelines scripts are installed
@@ -64,7 +66,7 @@ class AssetManager {
 
     /**
      * The pipeline name. It must be in the form {@code username/repo} where 'username'
-     * is a valid user name or organisation account, while 'repo' is the repository name
+     * is a valid user name or organization account, while 'repo' is the repository name
      * containing the pipeline code
      */
     private String project
@@ -422,7 +424,16 @@ class AssetManager {
     }
 
     String getDefaultBranch() {
-        getManifest().getDefaultBranch()
+        // if specified in manifest, that takes priority
+        // otherwise look for a symbolic ref (refs/remotes/origin/HEAD)
+        return getManifest().getDefaultBranch()
+                ?: getRemoteBranch()
+                ?: DEFAULT_BRANCH
+    }
+
+    protected String getRemoteBranch() {
+        Ref remoteHead = git.getRepository().findRef(REMOTE_DEFAULT_HEAD)
+        return remoteHead?.getTarget()?.getName()?.substring(REMOTE_REFS_ROOT.length())
     }
 
     @Memoized
@@ -582,7 +593,7 @@ class AssetManager {
             final cloneURL = getGitRepositoryUrl()
             log.debug "Pulling $project -- Using remote clone url: ${cloneURL}"
 
-            // clone it
+            // clone it, but don't specify a revision - jgit will checkout the default branch
             def clone = Git.cloneRepository()
             if( provider.hasCredentials() )
                 clone.setCredentialsProvider( provider.getGitCredentials() )
@@ -595,9 +606,25 @@ class AssetManager {
                 clone.setDepth(deep)
             clone.call()
 
+            // git cli would automatically create a 'refs/remotes/origin/HEAD' symbolic ref pointing at the remote's
+            // default branch. jgit doesn't do this, but since it automatically checked out the default branch on clone
+            // we can create the symbolic ref ourselves using the current head
+            def head = git.getRepository().findRef(Constants.HEAD)
+            if( head ) {
+                def headName = head.isSymbolic()
+                    ? Repository.shortenRefName(head.getTarget().getName())
+                    : head.getName()
+
+                git.repository.getRefDatabase()
+                    .newUpdate(REMOTE_DEFAULT_HEAD, true)
+                    .link(REMOTE_REFS_ROOT + headName)
+            } else {
+                log.debug "Unable to determine default branch of repo ${cloneURL}, symbolic ref not created"
+            }
+
+            // now the default branch is recorded in the repo, explicitly checkout the revision (if specified).
+            // this also allows 'revision' to be a SHA commit id, which isn't supported by the clone command
             if( revision ) {
-                // use an explicit checkout command *after* the clone instead of cloning a specific branch
-                // because the clone command does not allow the use of SHA commit id (only branch and tag names)
                 try { git.checkout() .setName(revision) .call() }
                 catch ( RefNotFoundException e ) { checkoutRemoteBranch(revision) }
             }
@@ -729,6 +756,9 @@ class AssetManager {
         }
     }
 
+    static boolean isRemoteBranch(Ref ref) {
+        return ref.name.startsWith(REMOTE_REFS_ROOT) && ref.name != REMOTE_DEFAULT_HEAD
+    }
 
     /**
      * @return A list of existing branches and tags names. For example
@@ -750,7 +780,7 @@ class AssetManager {
         def master = getDefaultBranch()
 
         List<String> branches = getBranchList()
-            .findAll { it.name.startsWith('refs/heads/') || it.name.startsWith('refs/remotes/origin/') }
+            .findAll { it.name.startsWith('refs/heads/') || isRemoteBranch(it) }
             .unique { shortenRefName(it.name) }
             .collect { Ref it -> refToString(it,current,master,false,level) }
 
@@ -785,7 +815,7 @@ class AssetManager {
 
         Map<String, Ref> remote = checkForUpdates ? git.lsRemote().callAsMap() : null
         getBranchList()
-                .findAll { it.name.startsWith('refs/heads/') || it.name.startsWith('refs/remotes/origin/') }
+                .findAll { it.name.startsWith('refs/heads/') || isRemoteBranch(it) }
                 .unique { shortenRefName(it.name) }
                 .each { Ref it -> branches << refToMap(it,remote)  }
 
@@ -803,7 +833,7 @@ class AssetManager {
 
     protected Map refToMap(Ref ref, Map<String,Ref> remote) {
         final entry = new HashMap(2)
-        final peel = git.getRepository().peel(ref)
+        final peel = git.getRepository().getRefDatabase().peel(ref)
         final objId = peel.getPeeledObjectId() ?: peel.getObjectId()
         // the branch or tag name
         entry.name = shortenRefName(ref.name)
@@ -837,7 +867,7 @@ class AssetManager {
         result << (name == current ? '*' : ' ')
 
         if( level ) {
-            def peel = git.getRepository().peel(ref)
+            def peel = git.getRepository().getRefDatabase().peel(ref)
             def obj = peel.getPeeledObjectId() ?: peel.getObjectId()
             result << ' '
             result << formatObjectId(obj, level == 1)
@@ -882,7 +912,7 @@ class AssetManager {
 
         def remote = git.lsRemote().callAsMap()
         List<String> branches = getBranchList()
-                .findAll { it.name.startsWith('refs/heads/') || it.name.startsWith('refs/remotes/origin/') }
+                .findAll { it.name.startsWith('refs/heads/') || isRemoteBranch(it) }
                 .unique { shortenRefName(it.name) }
                 .findAll { Ref ref -> hasRemoteChange(ref,remote) }
                 .collect { Ref ref -> formatUpdate(remote.get(ref.name),level) }
diff --git a/modules/nextflow/src/main/groovy/nextflow/scm/AzureRepositoryProvider.groovy b/modules/nextflow/src/main/groovy/nextflow/scm/AzureRepositoryProvider.groovy
index a8cb617bf9..8435099ebf 100644
--- a/modules/nextflow/src/main/groovy/nextflow/scm/AzureRepositoryProvider.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/scm/AzureRepositoryProvider.groovy
@@ -35,6 +35,7 @@ final class AzureRepositoryProvider extends RepositoryProvider {
 
     private String user
     private String repo
+    private String urlPath;
     private String continuationToken
 
     AzureRepositoryProvider(String project, ProviderConfig config=null) {
@@ -42,6 +43,7 @@ final class AzureRepositoryProvider extends RepositoryProvider {
         Azure repo format follows Organization/Project/Repository where Project can be optional
         If Project is not present then Repository is used as Project (and also as Repository)
          */
+        this.urlPath = project
         def tokens = project.tokenize('/')
         this.repo = tokens.removeLast()
         if( tokens.size() == 1){
@@ -164,7 +166,7 @@ final class AzureRepositoryProvider extends RepositoryProvider {
     /** {@inheritDoc} */
     @Override
     String getRepositoryUrl() {
-        "${config.server}/$project"
+        "${config.server}/${urlPath}"
     }
 
     /** {@inheritDoc} */
diff --git a/modules/nextflow/src/main/groovy/nextflow/scm/RepositoryProvider.groovy b/modules/nextflow/src/main/groovy/nextflow/scm/RepositoryProvider.groovy
index 96a959c569..dc87b2f827 100644
--- a/modules/nextflow/src/main/groovy/nextflow/scm/RepositoryProvider.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/scm/RepositoryProvider.groovy
@@ -73,11 +73,23 @@ abstract class RepositoryProvider {
         return this
     }
 
+    String getRevision() {
+        return this.revision
+    }
+
     RepositoryProvider setRevision(String revision) {
         this.revision = revision
         return this
     }
 
+    String getProject() {
+        return this.project
+    }
+
+    ProviderConfig getConfig() {
+        return this.config
+    }
+
     boolean hasCredentials() {
         getUser() && getPassword()
     }
@@ -241,8 +253,15 @@ abstract class RepositoryProvider {
         }
     }
 
-    @Memoized
     protected <T> List<T> invokeAndResponseWithPaging(String request, Closure<T> parse) {
+        // this is needed because apparently bytebuddy used by testing framework is not able
+        // to handle properly this method signature using both generics and `@Memoized` annotation.
+        // therefore the `@Memoized` has been moved to the inner method invocation
+        return invokeAndResponseWithPaging0(request, parse)
+    }
+
+    @Memoized
+    protected List invokeAndResponseWithPaging0(String request, Closure parse) {
         int page = 0
         final result = new ArrayList()
         while( true ) {
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/OutputDsl.groovy b/modules/nextflow/src/main/groovy/nextflow/script/OutputDsl.groovy
index d7bb9c4f09..79ed13cde0 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/OutputDsl.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/OutputDsl.groovy
@@ -21,6 +21,8 @@ import java.nio.file.Path
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import groovyx.gpars.dataflow.DataflowWriteChannel
+import nextflow.Global
+import nextflow.Session
 import nextflow.exception.ScriptRuntimeException
 import nextflow.extension.CH
 import nextflow.extension.MixOp
@@ -35,65 +37,15 @@ import nextflow.file.FileHelper
 @CompileStatic
 class OutputDsl {
 
-    private Map<String,Map> publishConfigs = [:]
+    private Session session = Global.session as Session
 
-    private Path directory
-
-    private Map defaults = [:]
+    private Map<String,Map> targetConfigs = [:]
 
     private volatile List<PublishOp> ops = []
 
-    void directory(String directory) {
-        if( this.directory )
-            throw new ScriptRuntimeException("Publish directory cannot be defined more than once in the workflow publish definition")
-        this.directory = FileHelper.toCanonicalPath(directory)
-    }
-
-    void contentType(String value) {
-        setDefault('contentType', value)
-    }
-
-    void contentType(boolean value) {
-        setDefault('contentType', value)
-    }
-
-    void ignoreErrors(boolean value) {
-        setDefault('ignoreErrors', value)
-    }
-
-    void mode(String value) {
-        setDefault('mode', value)
-    }
-
-    void overwrite(boolean value) {
-        setDefault('overwrite', value)
-    }
-
-    void overwrite(String value) {
-        setDefault('overwrite', value)
-    }
-
-    void storageClass(String value) {
-        setDefault('storageClass', value)
-    }
-
-    void tags(Map value) {
-        setDefault('tags', value)
-    }
-
-    void enabled( boolean value ) {
-        setDefault('enabled', value)
-    }
-
-    private void setDefault(String name, Object value) {
-        if( defaults.containsKey(name) )
-            throw new ScriptRuntimeException("Default `${name}` option cannot be defined more than once in the workflow publish definition")
-        defaults[name] = value
-    }
-
     void target(String name, Closure closure) {
-        if( publishConfigs.containsKey(name) )
-            throw new ScriptRuntimeException("Target '${name}' is defined more than once in the workflow publish definition")
+        if( targetConfigs.containsKey(name) )
+            throw new ScriptRuntimeException("Target '${name}' is defined more than once in the workflow output definition")
 
         final dsl = new TargetDsl()
         final cl = (Closure)closure.clone()
@@ -101,10 +53,12 @@ class OutputDsl {
         cl.setDelegate(dsl)
         cl.call()
 
-        publishConfigs[name] = dsl.getOptions()
+        targetConfigs[name] = dsl.getOptions()
     }
 
     void build(Map<DataflowWriteChannel,String> targets) {
+        final defaults = session.config.navigate('workflow.output', Collections.emptyMap()) as Map
+
         // construct mapping of target name -> source channels
         final Map<String,List<DataflowWriteChannel>> publishSources = [:]
         for( final source : targets.keySet() ) {
@@ -116,22 +70,27 @@ class OutputDsl {
             publishSources[name] << source
         }
 
+        // validate target configs
+        for( final name : targetConfigs.keySet() ) {
+            if( name !in publishSources )
+                log.warn "Publish target '${name}' was defined in the output block but not used by the workflow"
+        }
+
         // create publish op (and optional index op) for each target
         for( final name : publishSources.keySet() ) {
             final sources = publishSources[name]
             final mixed = sources.size() > 1
                 ? new MixOp(sources.collect( ch -> CH.getReadChannel(ch) )).apply()
                 : sources.first()
-            final opts = publishOptions(name, publishConfigs[name] ?: [:])
+            final overrides = targetConfigs[name] ?: Collections.emptyMap()
+            final opts = publishOptions(name, defaults, overrides)
 
-            ops << new PublishOp(CH.getReadChannel(mixed), opts).apply()
+            if( opts.enabled == null || opts.enabled )
+                ops << new PublishOp(CH.getReadChannel(mixed), opts).apply()
         }
     }
 
-    private Map publishOptions(String name, Map overrides) {
-        if( !directory )
-            directory = FileHelper.toCanonicalPath('.')
-
+    private Map publishOptions(String name, Map defaults, Map overrides) {
         final opts = defaults + overrides
         if( opts.containsKey('ignoreErrors') )
             opts.failOnError = !opts.remove('ignoreErrors')
@@ -139,9 +98,9 @@ class OutputDsl {
             opts.overwrite = 'standard'
 
         final path = opts.path as String ?: name
-        if( path.startsWith('/') )
-            throw new ScriptRuntimeException("Invalid publish target path '${path}' -- it should be a relative path")
-        opts.path = directory.resolve(path)
+        if( path.startsWith('/') || path.endsWith('/') )
+            throw new ScriptRuntimeException("Invalid publish target path '${path}' -- it should not contain a leading or trailing slash")
+        opts.path = session.outputDir.resolve(path)
 
         if( opts.index && !(opts.index as Map).path )
             throw new ScriptRuntimeException("Index file definition for publish target '${name}' is missing `path` option")
@@ -168,6 +127,10 @@ class OutputDsl {
             setOption('contentType', value)
         }
 
+        void enabled(boolean value) {
+            setOption('enabled', value)
+        }
+
         void ignoreErrors(boolean value) {
             setOption('ignoreErrors', value)
         }
@@ -197,6 +160,11 @@ class OutputDsl {
             setOption('path', value)
         }
 
+        void path(Closure value) {
+            setOption('path', '.')
+            setOption('pathAs', value)
+        }
+
         void storageClass(String value) {
             setOption('storageClass', value)
         }
@@ -205,10 +173,6 @@ class OutputDsl {
             setOption('tags', value)
         }
 
-        void enabled( boolean value ) {
-            setOption('enabled', value)
-        }
-
         private void setOption(String name, Object value) {
             if( opts.containsKey(name) )
                 throw new ScriptRuntimeException("Publish option `${name}` cannot be defined more than once for a given target")
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ProcessConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ProcessConfig.groovy
index e0c44db5db..84c52c3a91 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/ProcessConfig.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/ProcessConfig.groovy
@@ -127,7 +127,7 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
             debug: false,
             cacheable: true,
             shell: BashWrapperBuilder.BASH,
-            maxRetries: 0,
+            maxRetries: 1,
             maxErrors: -1,
             errorStrategy: ErrorStrategy.TERMINATE
     ]
@@ -165,11 +165,6 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
      */
     private outputs = new OutputsList()
 
-    /**
-     * Map of default publish targets
-     */
-    private Map<String,String> publishTargets = [:]
-
     /**
      * Initialize the taskConfig object with the defaults values
      *
@@ -519,13 +514,6 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
         outputs
     }
 
-    /**
-     * Typed shortcut to {@code #publishTargets}
-     */
-    Map<String,String> getPublishTargets() {
-        publishTargets
-    }
-
     /**
      * Implements the process {@code debug} directive.
      */
@@ -663,13 +651,6 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
         result
     }
 
-    void _publish_target(String emit, String name) {
-        final emitNames = outputs.collect { param -> param.channelEmitName }
-        if( emit !in emitNames )
-            throw new IllegalArgumentException("Invalid emit name '${emit}' in publish statement, valid emits are: ${emitNames.join(', ')}")
-        publishTargets[emit] = name
-    }
-
     /**
      * Defines a special *dummy* input parameter, when no inputs are
      * provided by the user for the current task
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ProcessDef.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ProcessDef.groovy
index f7e59b371e..ae95b230e3 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/ProcessDef.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/ProcessDef.groovy
@@ -18,7 +18,6 @@ package nextflow.script
 
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
-import groovyx.gpars.dataflow.DataflowWriteChannel
 import nextflow.Const
 import nextflow.Global
 import nextflow.Session
@@ -209,14 +208,6 @@ class ProcessDef extends BindableDef implements IterableDef, ChainableDef {
         // make a copy of the output list because execution can change it
         output = new ChannelOut(declaredOutputs.clone())
 
-        // register process publish targets
-        for( final entry : processConfig.getPublishTargets() ) {
-            final emit = entry.key
-            final name = entry.value
-            final source = (DataflowWriteChannel)output.getProperty(emit)
-            session.publishTargets[source] = name
-        }
-
         // create the executor
         final executor = session
                 .executorFactory
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ScriptBinding.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ScriptBinding.groovy
index e844ab82c4..9ef4999905 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/ScriptBinding.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/ScriptBinding.groovy
@@ -25,7 +25,6 @@ import groovy.util.logging.Slf4j
 import nextflow.NF
 import nextflow.Session
 import nextflow.exception.AbortOperationException
-import org.apache.commons.lang.StringUtils
 /**
  * Defines the script execution context. By default provided the following variables
  * <li>{@code __$session}: the current execution session
@@ -202,23 +201,17 @@ class ScriptBinding extends WorkflowBinding {
     }
 
     /**
-     * Holds parameter immutable values
+     * Implements immutable params map
      */
     @CompileStatic
     static class ParamsMap implements Map<String,Object> {
 
-        private Set<String> readOnlyNames
-
-        private List<String> realNames
-
         private List<String> scriptAssignment = []
 
         @Delegate
         private Map<String,Object> target
 
         ParamsMap() {
-            readOnlyNames = []
-            realNames = []
             target = new LinkedHashMap<>()
         }
 
@@ -227,23 +220,15 @@ class ScriptBinding extends WorkflowBinding {
             putAll(values)
         }
 
-        private ParamsMap(ParamsMap template, Map overrides) {
-            this(template)
-            allowNames(overrides.keySet())
-            putAll(overrides)
-        }
+        private ParamsMap(ParamsMap values, Map<String,?> overrides) {
+            this(values)
 
-        ParamsMap copyWith(Map overrides) {
-            return new ParamsMap(this, overrides)
+            for( def entry : overrides )
+                put0(entry.key, entry.value, true)
         }
 
-        private ParamsMap allowNames(Set names) {
-            for( String name : names ) {
-                final name2 = name.contains('-') ? hyphenToCamelCase(name) : camelCaseToHyphen(name)
-                readOnlyNames.remove(name)
-                readOnlyNames.remove(name2)
-            }
-            return this
+        ParamsMap copyWith(Map<String,?> overrides) {
+            return new ParamsMap(this, overrides)
         }
 
         @Override
@@ -269,142 +254,26 @@ class ScriptBinding extends WorkflowBinding {
         @Override
         String put(String name, Object value) {
             assert name
-            (name in scriptAssignment
-                    ? log.warn("`params.$name` is defined multiple times -- Assignments following the first are ignored")
-                    : scriptAssignment << name )
+            if( name in scriptAssignment )
+                log.warn("`params.$name` is defined multiple times -- Assignments following the first are ignored")
+            else
+                scriptAssignment << name
             return put0(name,value)
         }
 
-        private String put0(String name, Object value) {
-
-            // keep track of the real name
-            realNames << name
-
-            // normalize the name
-            def name2 = name.contains('-') ? hyphenToCamelCase(name) : camelCaseToHyphen(name)
-
-            final readOnly = name in readOnlyNames || name2 in readOnlyNames
-
-            def result = null
-            if( !readOnly ) {
-                readOnlyNames << name
-                readOnlyNames << name2
-                result = target.put(name, value)
-                target.put(name2, value)
-            }
-
-            return result
+        private String put0(String name, Object value, boolean allowOverride=false) {
+            return allowOverride || !target.containsKey(name)
+                ? target.put(name, value)
+                : null
         }
 
         @Override
-        void putAll(Map other) {
-            for( Entry<String,Object> entry : other.entrySet() ) {
+        void putAll(Map<? extends String,? extends Object> other) {
+            for( def entry : other.entrySet() ) {
                 put0(entry.getKey(), entry.getValue())
             }
         }
 
-        /**
-         * Renders a string containing all name-value pairs as a command line string
-         *
-         * @param opts String formatting options:
-         *   {@code sep}: the key-value pair separator
-         *   {@code quote}: the character to be used to quote the parameter value
-         *   {@code prefix}: the character(s) prepended to the parameter key
-         *
-         * @return A command line formatted string e.g. {@code --foo x --bar y}
-         */
-        String all(Map opts = null) {
-
-            String sep = opts?.sep ?: ' '
-            String quote = opts?.quote ?: ''
-            String prefix = opts?.prefix ?: '--'
-
-            def result = []
-            realNames.each {
-                result << ("$prefix$it$sep${wrap(this.get(it).toString(), quote)}".toString())
-            }
-            return result.join(' ')
-        }
-
-        /**
-         * Wrap a string value with quote characters
-         *
-         * @param str The string with value to be wrapped by quote characters
-         * @param quote The quote character
-         * @return The quoted string
-         */
-        @PackageScope
-        static String wrap( String str, String quote ) {
-            if( !quote && (str.contains(' ') || str.contains('"') || str.contains("'") ))
-                quote = '"'
-
-            if( !quote )
-                return str
-
-            def result = new StringBuilder()
-            result.append(quote)
-            str.each {
-                result.append( it == quote ? '\\'+quote : it )
-            }
-            result.append(quote)
-            return result.toString()
-        }
-
-        /**
-         *  Converts a string containing words separated by a hyphen character to a camelCase string
-         *
-         * @param str The string to be converted
-         * @return
-         */
-        @PackageScope
-        static String hyphenToCamelCase( String str ) {
-
-            if( !str ) { return str }
-
-            def result = new StringBuilder()
-            str.split('-').eachWithIndex{ String entry, int i ->
-                result << (i>0 ? StringUtils.capitalize(entry) : entry )
-            }
-
-            return result.toString()
-        }
-
-        /**
-         * Converts a camel-case string to a string where words are separated by hyphen character
-         *
-         * @param str The string to be converted
-         * @return A string where camel-case words are converted to words separated by hyphen character
-         */
-        @PackageScope
-        static String camelCaseToHyphen( String str ) {
-
-            def lower = 'a'..'z'
-            def upper = 'A'..'Z'
-
-            def result = new StringBuilder()
-            if( !str ) {
-                return str
-            }
-
-            result << str[0]
-            for( int i=1; i<str.size(); i++ ) {
-                if( str[i] in upper && str[i-1] in lower  ) {
-                    result << '-'
-                    if( i+1<str.size() && str[i+1] in lower ) {
-                        result << str[i].toLowerCase()
-                    }
-                    else {
-                        result << str[i]
-                    }
-                }
-                else {
-                    result << str[i]
-                }
-            }
-
-            return result.toString()
-        }
-
     }
 
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/WorkflowMetadata.groovy b/modules/nextflow/src/main/groovy/nextflow/script/WorkflowMetadata.groovy
index ed8023c5b3..770dd66969 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/WorkflowMetadata.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/WorkflowMetadata.groovy
@@ -140,6 +140,11 @@ class WorkflowMetadata {
      */
     Path launchDir
 
+    /**
+     * Workflow output directory
+     */
+    Path outputDir
+
     /**
      * Workflow working directory
      */
@@ -258,6 +263,7 @@ class WorkflowMetadata {
         this.container = session.fetchContainers()
         this.commandLine = session.commandLine
         this.nextflow = NextflowMeta.instance
+        this.outputDir = session.outputDir
         this.workDir = session.workDir
         this.launchDir = Paths.get('.').complete()
         this.profile = session.profile ?: ConfigBuilder.DEFAULT_PROFILE
diff --git a/modules/nextflow/src/main/groovy/nextflow/trace/ProgressRecord.groovy b/modules/nextflow/src/main/groovy/nextflow/trace/ProgressRecord.groovy
index 0e208f5736..8c73ce2318 100644
--- a/modules/nextflow/src/main/groovy/nextflow/trace/ProgressRecord.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/trace/ProgressRecord.groovy
@@ -63,7 +63,7 @@ class ProgressRecord implements Cloneable {
 
     int getTotalCount() {
         pending+ submitted+ running+
-           succeeded+ failed+ cached+ stored
+           succeeded+ failed+ cached+ stored + aborted
     }
 
     int getCompletedCount() {
diff --git a/modules/nextflow/src/main/groovy/nextflow/trace/TraceObserver.groovy b/modules/nextflow/src/main/groovy/nextflow/trace/TraceObserver.groovy
index 636ad03287..fd7dedc321 100644
--- a/modules/nextflow/src/main/groovy/nextflow/trace/TraceObserver.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/trace/TraceObserver.groovy
@@ -122,6 +122,13 @@ trait TraceObserver {
      */
     void onFlowError(TaskHandler handler, TraceRecord trace){}
 
+    /**
+     * Method that is invoked when a value is published from a channel.
+     *
+     * @param value
+     */
+    void onWorkflowPublish(Object value){}
+
     /**
      * Method that is invoke when an output file is published
      * into a `publishDir` folder.
diff --git a/modules/nextflow/src/main/groovy/nextflow/util/ArrayBag.groovy b/modules/nextflow/src/main/groovy/nextflow/util/ArrayBag.groovy
index 64e849085c..bd7dcff3b8 100644
--- a/modules/nextflow/src/main/groovy/nextflow/util/ArrayBag.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/util/ArrayBag.groovy
@@ -63,53 +63,66 @@ class ArrayBag<E> implements Bag<E>, List<E>, KryoSerializable {
         InvokerHelper.inspect(this)
     }
 
-//    E getAt( int index )  {
-//        target.get(index)
-//    }
-//
-//    void putAt( int index, E value ) {
-//        target.set(index, value)
-//    }
-//
-//    @Override
-//    int hashCode() {
-//        int h = 0;
-//        Iterator<E> i = target.iterator();
-//        while (i.hasNext()) {
-//            E obj = i.next();
-//            if (obj != null)
-//                h += obj.hashCode();
-//        }
-//        return h;
-//    }
-//
-//    @Override
-//    boolean equals(Object o) {
-//        if ( o.is(this) )
-//            return true;
-//
-//        if (!(o instanceof ArrayBag))
-//            return false;
-//
-//        Collection other = ((ArrayBag)o).target
-//        if (other.size() != target.size())
-//            return false;
-//
-//        try {
-//            return target.containsAll(other);
-//        }
-//        catch (ClassCastException unused)   {
-//            return false;
-//        }
-//        catch (NullPointerException unused) {
-//            return false;
-//        }
-//    }
+    @Override
+    int hashCode() {
+        int h = 0;
+        Iterator<E> i = target.iterator();
+        while (i.hasNext()) {
+            E obj = i.next();
+            if (obj != null)
+                h += obj.hashCode();
+        }
+        return h;
+    }
+
+    /**
+     * NOTE!!! this method implements an equality is NOT used when invoking `equals` method
+     * or using `==` operator from Groovy code. This because the Groovy runtime implements its
+     * own equality logic both for {@link Map} and {@link Collection} logic.
+     *
+     * See
+     * https://issues.apache.org/jira/browse/GROOVY-9003
+     *
+     * However this is still applied when equality is checked by Java compiled code e.g. Java SDK.
+     * For this reason is necessary to implement the expected equals (and hashCode) semantic by `join`
+     * (and other) operators.
+     *
+     * See issue
+     * https://github.com/nextflow-io/nextflow/issues/5187
+     *
+     * @return
+     *      {@code true} is the content of the bag is equals to another bag irrespective the elements order,
+     *      {@code false} otherwise
+     */
+    @Override
+    boolean equals(Object o) {
+        if ( o.is(this) )
+            return true;
+
+        if (!(o instanceof ArrayBag))
+            return false;
 
+        Collection other = ((ArrayBag)o).target
+        if (other.size() != target.size())
+            return false;
+
+        try {
+            return target.containsAll(other);
+        }
+        catch (ClassCastException unused)   {
+            return false;
+        }
+        catch (NullPointerException unused) {
+            return false;
+        }
+    }
+
+    @Override
     void read (Kryo kryo, Input input) {
         target = kryo.readObject(input,ArrayList)
     }
 
+    @Override
     void write (Kryo kryo, Output output) {
         kryo.writeObject(output, target)
     }
diff --git a/modules/nextflow/src/main/groovy/nextflow/util/ConfigHelper.groovy b/modules/nextflow/src/main/groovy/nextflow/util/ConfigHelper.groovy
index f128585a71..d077760614 100644
--- a/modules/nextflow/src/main/groovy/nextflow/util/ConfigHelper.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/util/ConfigHelper.groovy
@@ -18,10 +18,14 @@ package nextflow.util
 
 import java.nio.file.Path
 
+import groovy.json.JsonOutput
 import groovy.transform.CompileStatic
 import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
+import nextflow.config.ConfigClosurePlaceholder
 import org.codehaus.groovy.runtime.InvokerHelper
+import org.yaml.snakeyaml.DumperOptions
+import org.yaml.snakeyaml.Yaml
 /**
  * Helper method to handle configuration object
  *
@@ -301,6 +305,19 @@ class ConfigHelper {
         flattenFormat(map.toConfigObject(), sort)
     }
 
+    static String toJsonString(ConfigObject config, boolean sort=false) {
+        final copy = normaliseConfig(config)
+        JsonOutput.prettyPrint(JsonOutput.toJson(sort ? deepSort(copy) : copy))
+    }
+
+    static String toYamlString(ConfigObject config, boolean sort=false) {
+        final copy = normaliseConfig(config)
+        final options = new DumperOptions();
+        options.setDefaultFlowStyle(DumperOptions.FlowStyle.BLOCK); // Use block style instead of inline
+        final yaml = new Yaml(options)
+        return yaml.dump(sort ? deepSort(copy) : copy);
+    }
+
     static boolean isValidIdentifier(String s) {
         // an empty or null string cannot be a valid identifier
         if (s == null || s.length() == 0) {
@@ -321,7 +338,50 @@ class ConfigHelper {
         return true;
     }
 
+    private static Map<String, Object> deepSort(Map<String, Object> map) {
+        Map<String, Object> sortedMap = new TreeMap<>(map);  // Sort current map
+
+        for (Map.Entry<String, Object> entry : sortedMap.entrySet()) {
+            Object value = entry.getValue();
+            if (value instanceof Map) {
+                // Recursively sort nested map
+                sortedMap.put(entry.getKey(), deepSort((Map<String, Object>) value));
+            }
+        }
+        return sortedMap;
+    }
 
+    private static Map<String,Object> normaliseConfig(ConfigObject config) {
+        final result = new LinkedHashMap()
+        for( Map.Entry it : config ) {
+            if( it.value instanceof Map && !it.value )
+                continue
+            result.put(it.key, normaliseObject0(it.value))
+        }
+        return result
+    }
 
+    private static Object normaliseObject0(Object value) {
+        if( value instanceof Map ) {
+            final map = value as Map
+            final ret = new LinkedHashMap(map.size())
+            for( Map.Entry entry : map.entrySet() ) {
+                ret.put(entry.key, normaliseObject0(entry.value))
+            }
+            return ret
+        }
+        if( value instanceof Collection ) {
+            final lis = value as List
+            final ret = new ArrayList(lis.size())
+            for( Object it : lis )
+                ret.add(normaliseObject0(it))
+            return ret
+        }
+        else if( value instanceof ConfigClosurePlaceholder ) {
+            return value.toString()
+        }
+        else
+            return value
+    }
 }
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy b/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy
index fc8bd68841..9a23cd77fd 100644
--- a/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy
@@ -16,10 +16,6 @@
 
 package nextflow.util
 
-import ch.qos.logback.core.encoder.Encoder
-import ch.qos.logback.core.spi.FilterAttachable
-import ch.qos.logback.core.spi.LifeCycle
-
 import static nextflow.Const.*
 
 import java.lang.reflect.Field
@@ -28,6 +24,7 @@ import java.nio.file.FileAlreadyExistsException
 import java.nio.file.NoSuchFileException
 import java.nio.file.Path
 import java.util.concurrent.atomic.AtomicBoolean
+import java.util.concurrent.atomic.AtomicInteger
 import java.util.regex.Pattern
 
 import ch.qos.logback.classic.Level
@@ -42,13 +39,16 @@ import ch.qos.logback.core.ConsoleAppender
 import ch.qos.logback.core.CoreConstants
 import ch.qos.logback.core.FileAppender
 import ch.qos.logback.core.LayoutBase
+import ch.qos.logback.core.encoder.Encoder
 import ch.qos.logback.core.encoder.LayoutWrappingEncoder
 import ch.qos.logback.core.filter.Filter
 import ch.qos.logback.core.joran.spi.NoAutoStart
 import ch.qos.logback.core.rolling.FixedWindowRollingPolicy
 import ch.qos.logback.core.rolling.RollingFileAppender
 import ch.qos.logback.core.rolling.TriggeringPolicyBase
+import ch.qos.logback.core.spi.FilterAttachable
 import ch.qos.logback.core.spi.FilterReply
+import ch.qos.logback.core.spi.LifeCycle
 import ch.qos.logback.core.util.FileSize
 import groovy.transform.CompileStatic
 import groovy.transform.PackageScope
@@ -85,6 +85,10 @@ import org.slf4j.MarkerFactory
 @CompileStatic
 class LoggerHelper {
 
+    static volatile boolean aborted
+
+    static final AtomicInteger errCount = new AtomicInteger()
+
     static private Logger log = LoggerFactory.getLogger(LoggerHelper)
 
     static public Marker STICKY = MarkerFactory.getMarker('sticky')
@@ -367,6 +371,36 @@ class LoggerHelper {
         INSTANCE.setQuiet0(quiet)
     }
 
+    /**
+     * Setup a minimal logger that redirect log events to stderr only used during app bootstrap
+     */
+    static void bootstrapLogger() {
+        LoggerContext context = (LoggerContext) LoggerFactory.getILoggerFactory();
+
+        // Reset the logger context (this clears any existing loggers)
+        context.reset();
+
+        // Create a console appender that writes to stderr
+        final consoleAppender = new ConsoleAppender<ILoggingEvent>();
+        consoleAppender.setContext(context);
+        consoleAppender.setTarget("System.err");
+
+        // Set a simple pattern for the log output
+        final encoder = new PatternLayoutEncoder();
+        encoder.setContext(context);
+        encoder.setPattern("%d{HH:mm:ss.SSS} %-5level - %msg%n");
+        encoder.start();
+
+        // Attach the encoder to the appender
+        consoleAppender.setEncoder(encoder);
+        consoleAppender.start();
+
+        // Get the root logger and set its level to DEBUG
+        Logger rootLogger = context.getLogger(Logger.ROOT_LOGGER_NAME);
+        rootLogger.addAppender(consoleAppender)
+        rootLogger.setLevel(Level.DEBUG)
+    }
+
     /*
      * Filters the logging event based on the level assigned to a specific 'package'
      */
@@ -389,6 +423,10 @@ class LoggerHelper {
                 return FilterReply.NEUTRAL;
             }
 
+            // print to console only the very first error log and ignore the others
+            if( aborted && event.level==Level.ERROR && errCount.getAndIncrement()>0 )
+                return FilterReply.DENY;
+
             def logger = event.getLoggerName()
             def level = event.getLevel()
             for( int i=0; i<len; i++ ) {
diff --git a/modules/nextflow/src/main/groovy/nextflow/util/NameGenerator.groovy b/modules/nextflow/src/main/groovy/nextflow/util/NameGenerator.groovy
index 8877622f0c..d5a0f62a59 100644
--- a/modules/nextflow/src/main/groovy/nextflow/util/NameGenerator.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/util/NameGenerator.groovy
@@ -412,6 +412,9 @@ class NameGenerator {
             // David Hilbert - German mathematician, recognized as one of the most influential and universal mathematicians of the 19th and early 20th centuries. he is known as one of the founders of proof theory and mathematical logic, as well as for being among the first to distinguish between mathematics and metamathematics. https://en.wikipedia.org/wiki/David_Hilbert
             "hilbert",
 
+            // Rahel Hirsch - German physician, the first woman in the Kingdom of Prussia to be appointed a professor of medicine. https://en.wikipedia.org/wiki/Rahel_Hirsch
+            "hirsch",
+
             // Dorothy Hodgkin was a British biochemist, credited with the development of protein crystallography. She was awarded the Nobel Prize in Chemistry in 1964. https://en.wikipedia.org/wiki/Dorothy_Hodgkin
             "hodgkin",
 
@@ -628,6 +631,9 @@ class NameGenerator {
             // Robert Noyce invented silicone integrated circuits and gave Silicon Valley its name. https://en.wikipedia.org/wiki/Robert_Noyce
             "noyce",
 
+            // Severo Ochoa was a Spanish physician and biochemist, best known for being the winner of the 1959 Nobel Prize in Physiology or Medicine together with Arthur Kornberg for their discovery of the mechanisms in the biological synthesis of RNA and DNA. https://en.wikipedia.org/wiki/Severo_Ochoa
+            "ochoa",
+
             // Pāṇini - Ancient Indian linguist and grammarian from 4th century CE who worked on the world's first formal system. https://en.wikipedia.org/wiki/P%C4%81%E1%B9%87ini#Comparison_with_modern_formal_systems
             "panini",
 
@@ -700,6 +706,9 @@ class NameGenerator {
             // Meghnad Saha - Indian astrophysicist best known for his development of the Saha equation, used to describe chemical and physical conditions in stars. https://en.wikipedia.org/wiki/Meghnad_Saha
             "saha",
 
+            // Margarita Salas - Spanish biochemist and molecular biologist, best known for her discovery and characterisation of the Φ29 phage DNA polymerase. https://en.wikipedia.org/wiki/Margarita_Salas
+            "salas",
+
             // Jean E. Sammet developed FORMAC, the first widely used computer language for symbolic manipulation of mathematical formulas. https://en.wikipedia.org/wiki/Jean_E._Sammet
             "sammet",
 
diff --git a/modules/nextflow/src/main/resources/META-INF/build-info.properties b/modules/nextflow/src/main/resources/META-INF/build-info.properties
index 4365a054ab..2053248f03 100644
--- a/modules/nextflow/src/main/resources/META-INF/build-info.properties
+++ b/modules/nextflow/src/main/resources/META-INF/build-info.properties
@@ -1,4 +1,4 @@
-build=5921
-version=24.07.0-edge
-timestamp=1722884291592
-commitId=e8d643c2f
+build=5929
+version=24.11.0-edge
+timestamp=1733218258400
+commitId=7e2c8d82b
diff --git a/modules/nextflow/src/main/resources/META-INF/plugins-info.txt b/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
index f76e2fd995..c650c71066 100644
--- a/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
+++ b/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
@@ -1,8 +1,8 @@
-nf-amazon@2.7.0
-nf-azure@1.8.1
+nf-amazon@2.10.0
+nf-azure@1.11.0
 nf-cloudcache@0.4.2
 nf-codecommit@0.2.2
 nf-console@1.1.4
-nf-google@1.14.0
-nf-tower@1.9.2
-nf-wave@1.5.0
\ No newline at end of file
+nf-google@1.16.0
+nf-tower@1.9.3
+nf-wave@1.8.0
\ No newline at end of file
diff --git a/modules/nextflow/src/main/resources/nextflow/dag/mermaid.dag.template.html b/modules/nextflow/src/main/resources/nextflow/dag/mermaid.dag.template.html
index 9bb91c48b0..0ab1d9475e 100644
--- a/modules/nextflow/src/main/resources/nextflow/dag/mermaid.dag.template.html
+++ b/modules/nextflow/src/main/resources/nextflow/dag/mermaid.dag.template.html
@@ -19,11 +19,25 @@
 </head>
 <body>
 <pre class="mermaid" style="text-align: center;">
+%%{
+  init: {
+    'theme': 'base',
+    'themeVariables': {
+      'primaryColor': '#B6ECE2',
+      'primaryTextColor': '#160F26',
+      'primaryBorderColor': '#065647',
+      'lineColor': '#545555',
+      'clusterBkg': '#BABCBD22',
+      'clusterBorder': '#DDDEDE',
+      'fontFamily': 'arial'
+    }
+  }
+}%%
 REPLACE_WITH_NETWORK_DATA
 </pre>
 <script type="module">
   import mermaid from 'https://cdn.jsdelivr.net/npm/mermaid@10/dist/mermaid.esm.min.mjs';
-  mermaid.initialize({ startOnLoad: true });
+  mermaid.initialize({ startOnLoad: true, maxTextSize: Number.MAX_SAFE_INTEGER, maxEdges: Number.MAX_SAFE_INTEGER });
 </script>
 </body>
 </html>
diff --git a/modules/nextflow/src/main/resources/nextflow/executor/command-run.txt b/modules/nextflow/src/main/resources/nextflow/executor/command-run.txt
index 2bf34b617a..26cbf6a829 100644
--- a/modules/nextflow/src/main/resources/nextflow/executor/command-run.txt
+++ b/modules/nextflow/src/main/resources/nextflow/executor/command-run.txt
@@ -99,7 +99,13 @@ nxf_fs_fcp() {
 }
 
 on_exit() {
-    exit_status=${nxf_main_ret:=$?}
+    ## Capture possible errors.
+    ## Can be caused either by the task script, unstage script or after script if defined
+    local last_err=$?
+    ## capture the task error first or fallback to unstage error
+    local exit_status=${nxf_main_ret:=0}
+    [[ ${exit_status} -eq 0 && ${nxf_unstage_ret:=0} -ne 0 ]] && exit_status=${nxf_unstage_ret:=0}
+    [[ ${exit_status} -eq 0 && ${last_err} -ne 0 ]] && exit_status=${last_err}
     printf -- $exit_status {{exit_file}}
     set +u
     {{cleanup_cmd}}
@@ -121,13 +127,26 @@ nxf_stage() {
     {{stage_inputs}}
 }
 
-nxf_unstage() {
+nxf_unstage_outputs() {
     true
-    {{unstage_controls}}
-    [[ ${nxf_main_ret:=0} != 0 ]] && return
     {{unstage_outputs}}
 }
 
+nxf_unstage_controls() {
+    true
+    {{unstage_controls}}
+}
+
+nxf_unstage() {
+    ## Deactivate fast failure to allow uploading stdout and stderr files later
+    if [[ ${nxf_main_ret:=0} == 0 ]]; then
+        ## Data unstaging redirecting stdout and stderr with append mode
+        (set -e -o pipefail; (nxf_unstage_outputs | tee -a {{stdout_file}}) 3>&1 1>&2 2>&3 | tee -a {{stderr_file}})
+        nxf_unstage_ret=$?
+    fi
+    nxf_unstage_controls
+}
+
 nxf_main() {
     trap on_exit EXIT
     trap on_term TERM INT USR2
diff --git a/modules/nextflow/src/main/resources/nextflow/executor/command-trace.txt b/modules/nextflow/src/main/resources/nextflow/executor/command-trace.txt
index 8b5b2195f6..cf9d0b5d77 100644
--- a/modules/nextflow/src/main/resources/nextflow/executor/command-trace.txt
+++ b/modules/nextflow/src/main/resources/nextflow/executor/command-trace.txt
@@ -114,26 +114,28 @@ nxf_mem_watch() {
     done
 
     ## result struct: pid %mem vmem rss peak_vmem peak_rss
-    echo "%mem=${nxf_stat_ret[1]}"      >> $trace_file
-    echo "vmem=${nxf_stat_ret[2]}"      >> $trace_file
-    echo "rss=${nxf_stat_ret[3]}"       >> $trace_file
-    echo "peak_vmem=${nxf_stat_ret[4]}" >> $trace_file
-    echo "peak_rss=${nxf_stat_ret[5]}"  >> $trace_file
-    echo "vol_ctxt=${nxf_stat_ret[6]}"  >> $trace_file
-    echo "inv_ctxt=${nxf_stat_ret[7]}"  >> $trace_file
+    printf "%s\n" \
+        "%mem=${nxf_stat_ret[1]}" \
+        "vmem=${nxf_stat_ret[2]}" \
+        "rss=${nxf_stat_ret[3]}" \
+        "peak_vmem=${nxf_stat_ret[4]}" \
+        "peak_rss=${nxf_stat_ret[5]}" \
+        "vol_ctxt=${nxf_stat_ret[6]}" \
+        "inv_ctxt=${nxf_stat_ret[7]}" >> "$trace_file" || >&2 echo "Error: Failed to append to file: $trace_file"
 }
 
 nxf_write_trace() {
-    echo "nextflow.trace/v2"           > $trace_file
-    echo "realtime=$wall_time"         >> $trace_file
-    echo "%cpu=$ucpu"                  >> $trace_file
-    echo "cpu_model=$cpu_model"        >> $trace_file
-    echo "rchar=${io_stat1[0]}"        >> $trace_file
-    echo "wchar=${io_stat1[1]}"        >> $trace_file
-    echo "syscr=${io_stat1[2]}"        >> $trace_file
-    echo "syscw=${io_stat1[3]}"        >> $trace_file
-    echo "read_bytes=${io_stat1[4]}"   >> $trace_file
-    echo "write_bytes=${io_stat1[5]}"  >> $trace_file
+    printf "%s\n" \
+        "nextflow.trace/v2" \
+        "realtime=$wall_time" \
+        "%cpu=$ucpu" \
+        "cpu_model=$cpu_model" \
+        "rchar=${io_stat1[0]}" \
+        "wchar=${io_stat1[1]}" \
+        "syscr=${io_stat1[2]}" \
+        "syscw=${io_stat1[3]}" \
+        "read_bytes=${io_stat1[4]}" \
+        "write_bytes=${io_stat1[5]}" > "$trace_file" || >&2 echo "Error: Failed to write to file: $trace_file"
 }
 
 nxf_trace_mac() {
@@ -199,16 +201,17 @@ nxf_trace_linux() {
     local wall_time=$((end_millis-start_millis))
     [ $NXF_DEBUG = 1 ] && echo "+++ STATS %CPU=$ucpu TIME=$wall_time I/O=${io_stat1[*]}"
 
-    echo "nextflow.trace/v2"           > $trace_file
-    echo "realtime=$wall_time"         >> $trace_file
-    echo "%cpu=$ucpu"                  >> $trace_file
-    echo "cpu_model=$cpu_model"        >> $trace_file
-    echo "rchar=${io_stat1[0]}"        >> $trace_file
-    echo "wchar=${io_stat1[1]}"        >> $trace_file
-    echo "syscr=${io_stat1[2]}"        >> $trace_file
-    echo "syscw=${io_stat1[3]}"        >> $trace_file
-    echo "read_bytes=${io_stat1[4]}"   >> $trace_file
-    echo "write_bytes=${io_stat1[5]}"  >> $trace_file
+    printf "%s\n" \
+        "nextflow.trace/v2" \
+        "realtime=$wall_time" \
+        "%cpu=$ucpu" \
+        "cpu_model=$cpu_model" \
+        "rchar=${io_stat1[0]}" \
+        "wchar=${io_stat1[1]}" \
+        "syscr=${io_stat1[2]}" \
+        "syscw=${io_stat1[3]}" \
+        "read_bytes=${io_stat1[4]}" \
+        "write_bytes=${io_stat1[5]}" > "$trace_file" || >&2 echo "Error: Failed to write to file: $trace_file"
 
     ## join nxf_mem_watch
     [ -e /proc/$mem_proc ] && eval "echo 'DONE' >&$mem_fd" || true
diff --git a/modules/nextflow/src/test/groovy/nextflow/ChannelTest.groovy b/modules/nextflow/src/test/groovy/nextflow/ChannelTest.groovy
index e954c4bbcc..c7b45a6395 100644
--- a/modules/nextflow/src/test/groovy/nextflow/ChannelTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/ChannelTest.groovy
@@ -990,4 +990,23 @@ class ChannelTest extends Specification {
 
     }
 
+    def 'should not fail when setting SRA correct properties' () {
+        given:
+        def id = 'SRR389222'
+        def retryPolicy = [maxAttempts: 2]
+
+        when:
+        def result = Channel.fromSRA(id, apiKey: '1234', retryPolicy: retryPolicy, cache: false, max: 10, protocol: 'http')
+        then:
+        result != null
+
+    }
+
+    def 'should fail when SRA incorrect property' () {
+        when:
+        def result = Channel.fromSRA('SRR389222', incorrectKey: '1234')
+        then:
+        thrown(IllegalArgumentException)
+    }
+
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/NextflowTest.groovy b/modules/nextflow/src/test/groovy/nextflow/NextflowTest.groovy
index c32a461ecb..f49db65779 100644
--- a/modules/nextflow/src/test/groovy/nextflow/NextflowTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/NextflowTest.groovy
@@ -35,6 +35,17 @@ class NextflowTest extends Specification {
         System.getenv('CI_GROOVY_VERSION') == GroovySystem.getVersion()
     }
 
+    def 'should get an environment variable' () {
+        given:
+        SysEnv.push(FOO: 'FOO_VALUE')
+
+        expect:
+        Nextflow.env('FOO') == 'FOO_VALUE'
+
+        cleanup:
+        SysEnv.pop()
+    }
+
     def testFile() {
         expect:
         Nextflow.file('file.log').toFile() == new File('file.log').canonicalFile
diff --git a/modules/nextflow/src/test/groovy/nextflow/SessionTest.groovy b/modules/nextflow/src/test/groovy/nextflow/SessionTest.groovy
index fbcb3469e6..edcf06c4ff 100644
--- a/modules/nextflow/src/test/groovy/nextflow/SessionTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/SessionTest.groovy
@@ -601,16 +601,22 @@ class SessionTest extends Specification {
 
     }
 
+    @Unroll
     def 'should get module binaries status'() {
         given:
-        def session = new Session(CONFIG)
+        def session = new Session()
+        NextflowMeta.instance.moduleBinaries(MODE)
 
         expect:
         session.enableModuleBinaries() == EXPECTED
-        
+
+        cleanup:
+        NextflowMeta.instance.moduleBinaries(false)
+
         where:
-        CONFIG                                      | EXPECTED
-        [:]                                         | false
-        [nextflow:[enable:[moduleBinaries: true]]]  | true
+        MODE  | EXPECTED
+        false | false
+        true  | true
+
     }
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/CmdConfigTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/CmdConfigTest.groovy
index 232332b52b..a2f97b7496 100644
--- a/modules/nextflow/src/test/groovy/nextflow/cli/CmdConfigTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/cli/CmdConfigTest.groovy
@@ -90,6 +90,7 @@ class CmdConfigTest extends Specification {
                 .stripIndent().leftTrim()
 
     }
+
     def 'should canonical notation' () {
 
         given:
@@ -196,6 +197,86 @@ class CmdConfigTest extends Specification {
 
     }
 
+    def 'should print config using json' () {
+        given:
+        ByteArrayOutputStream buffer
+        ConfigObject config
+        def cmd = new CmdConfig(sort: true)
+
+        when:
+        buffer = new ByteArrayOutputStream()
+
+        config = new ConfigObject()
+        config.process.executor = 'slurm'
+        config.process.queue = 'long'
+        config.docker.enabled = true
+        config.dummy = new ConfigObject() // <-- empty config object should not be print
+        config.mail.from = 'yo@mail.com'
+        config.mail.smtp.host = 'mail.com'
+        config.mail.smtp.port = 25
+        config.mail.smtp.user = 'yo'
+
+        cmd.printJson0(config, buffer)
+        then:
+        buffer.toString() == '''\
+                    {
+                        "docker": {
+                            "enabled": true
+                        },
+                        "mail": {
+                            "from": "yo@mail.com",
+                            "smtp": {
+                                "host": "mail.com",
+                                "port": 25,
+                                "user": "yo"
+                            }
+                        },
+                        "process": {
+                            "executor": "slurm",
+                            "queue": "long"
+                        }
+                    }
+                    '''
+                    .stripIndent()
+    }
+
+    def 'should print config using yaml' () {
+        given:
+        ByteArrayOutputStream buffer
+        ConfigObject config
+        def cmd = new CmdConfig(sort: true)
+
+        when:
+        buffer = new ByteArrayOutputStream()
+
+        config = new ConfigObject()
+        config.process.executor = 'slurm'
+        config.process.queue = 'long'
+        config.docker.enabled = true
+        config.dummy = new ConfigObject() // <-- empty config object should not be print
+        config.mail.from = 'yo@mail.com'
+        config.mail.smtp.host = 'mail.com'
+        config.mail.smtp.port = 25
+        config.mail.smtp.user = 'yo'
+
+        cmd.printYaml0(config, buffer)
+        then:
+        buffer.toString() == '''\
+                    docker:
+                      enabled: true
+                    mail:
+                      from: yo@mail.com
+                      smtp:
+                        host: mail.com
+                        port: 25
+                        user: yo
+                    process:
+                      executor: slurm
+                      queue: long
+                    '''
+                    .stripIndent()
+    }
+
     def 'should parse config file' () {
         given:
         def folder = Files.createTempDirectory('test')
@@ -409,4 +490,101 @@ class CmdConfigTest extends Specification {
         folder?.deleteDir()
         SysEnv.pop()
     }
+
+    def 'should render json config output' () {
+        given:
+        def folder = Files.createTempDirectory('test')
+        def CONFIG = folder.resolve('nextflow.config')
+
+        CONFIG.text = '''
+        manifest {
+            author = 'me'
+            mainScript = 'foo.nf'
+        }
+        
+        process {
+          cpus = 4 
+          queue = 'cn-el7'
+          memory = { 10.GB }   
+          ext.other = { 10.GB * task.attempt }
+        }
+        '''
+        def buffer = new ByteArrayOutputStream()
+        // command definition
+        def cmd = new CmdConfig(outputFormat: 'json')
+        cmd.launcher = new Launcher(options: new CliOptions(config: [CONFIG.toString()]))
+        cmd.stdout = buffer
+        cmd.args = [ '.' ]
+
+        when:
+        cmd.run()
+
+        then:
+        buffer.toString() == '''
+        {
+            "manifest": {
+                "author": "me",
+                "mainScript": "foo.nf"
+            },
+            "process": {
+                "cpus": 4,
+                "queue": "cn-el7",
+                "memory": "{ 10.GB }",
+                "ext": {
+                    "other": "{ 10.GB * task.attempt }"
+                }
+            }
+        }
+        '''
+            .stripIndent().leftTrim()
+
+        cleanup:
+        folder.deleteDir()
+    }
+
+    def 'should render yaml config output' () {
+        given:
+        def folder = Files.createTempDirectory('test')
+        def CONFIG = folder.resolve('nextflow.config')
+
+        CONFIG.text = '''
+        manifest {
+            author = 'me'
+            mainScript = 'foo.nf'
+        }
+        
+        process {
+          cpus = 4 
+          queue = 'cn-el7'
+          memory = { 10.GB }   
+          ext.other = { 10.GB * task.attempt }
+        }
+        '''
+        def buffer = new ByteArrayOutputStream()
+        // command definition
+        def cmd = new CmdConfig(outputFormat: 'yaml')
+        cmd.launcher = new Launcher(options: new CliOptions(config: [CONFIG.toString()]))
+        cmd.stdout = buffer
+        cmd.args = [ '.' ]
+
+        when:
+        cmd.run()
+
+        then:
+        buffer.toString() == '''
+            manifest:
+              author: me
+              mainScript: foo.nf
+            process:
+              cpus: 4
+              queue: cn-el7
+              memory: '{ 10.GB }'
+              ext:
+                other: '{ 10.GB * task.attempt }'
+            '''
+                .stripIndent().leftTrim()
+
+        cleanup:
+        folder.deleteDir()
+    }
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/CmdInfoTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/CmdInfoTest.groovy
index ab2be742bd..e8949c946d 100644
--- a/modules/nextflow/src/test/groovy/nextflow/cli/CmdInfoTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/cli/CmdInfoTest.groovy
@@ -71,6 +71,7 @@ class CmdInfoTest extends Specification {
         screen.contains(" main script : main.nf")
         screen.contains(" revisions   : ")
         screen.contains(" * master (default)")
+        !screen.contains("   HEAD")
     }
 
     def 'should print json info' () {
@@ -89,11 +90,12 @@ class CmdInfoTest extends Specification {
         json.repository == "https://github.com/nextflow-io/hello"
         json.localPath == "$tempDir/nextflow-io/hello"
         json.manifest.mainScript == 'main.nf'
-        json.manifest.defaultBranch == 'master'
+        json.manifest.defaultBranch == null
         json.revisions.current == 'master'
         json.revisions.master == 'master'
         json.revisions.branches.size()>1
         json.revisions.branches.any { it.name == 'master' }
+        !json.revisions.branches.any { it.name == 'HEAD' }
         json.revisions.tags.size()>1
         json.revisions.tags.any { it.name == 'v1.1' }
 
@@ -115,11 +117,12 @@ class CmdInfoTest extends Specification {
         json.repository == "https://github.com/nextflow-io/hello"
         json.localPath == "$tempDir/nextflow-io/hello"
         json.manifest.mainScript == 'main.nf'
-        json.manifest.defaultBranch == 'master'
+        json.manifest.defaultBranch == null
         json.revisions.current == 'master'
         json.revisions.master == 'master'
         json.revisions.branches.size()>1
         json.revisions.branches.any { it.name == 'master' }
+        !json.revisions.branches.any { it.name == 'HEAD' }
         json.revisions.tags.size()>1
         json.revisions.tags.any { it.name == 'v1.1' }
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/CmdInspectTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/CmdInspectTest.groovy
deleted file mode 100644
index 5f76ecf033..0000000000
--- a/modules/nextflow/src/test/groovy/nextflow/cli/CmdInspectTest.groovy
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
- * Copyright 2013-2024, Seqera Labs
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package nextflow.cli
-
-
-import spock.lang.Specification
-import spock.lang.Unroll
-/**
- *
- * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
- */
-class CmdInspectTest extends Specification {
-
-    @Unroll
-    def 'should ask for confirmation' () {
-        given:
-        def cmd = Spy(new CmdInspect(concretize: CONCRETIZE))
-        Map wave
-
-        when:
-        wave = WAVE
-        cmd.checkWaveConfig(wave)
-        then:
-        wave == EXPECTED
-
-        where:
-        WAVE                            | CONCRETIZE    | EXPECTED
-        [:]                             | false         | [:]
-        [:]                             | true          | [:]
-        and:
-        [enabled:true]                  | false         | [enabled:true]
-        [enabled:true]                  | true          | [enabled:true]
-        and:
-        [enabled:true, freeze: true]    | false         | [enabled:true, freeze:true, dryRun: true]
-        [enabled:true, freeze: true]    | true          | [enabled:true, freeze:true, dryRun: false]
-
-    }
-
-}
diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/CmdRunTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/CmdRunTest.groovy
index 426890ef99..2de2397181 100644
--- a/modules/nextflow/src/test/groovy/nextflow/cli/CmdRunTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/cli/CmdRunTest.groovy
@@ -19,6 +19,7 @@ package nextflow.cli
 
 import java.nio.file.Files
 
+import nextflow.NextflowMeta
 import nextflow.SysEnv
 import nextflow.config.ConfigMap
 import nextflow.exception.AbortOperationException
@@ -94,6 +95,36 @@ class CmdRunTest extends Specification {
         [:]             | /x.y\.z/  | 'Hola'    | ['x': ['y.z': 'Hola']]
     }
 
+    def 'should convert cli params from kebab case to camel case' () {
+
+        when:
+        def params = [:]
+        CmdRun.addParam0(params, 'alphaBeta', 1)
+        CmdRun.addParam0(params, 'alpha-beta', 10)
+        then:
+        params['alphaBeta'] == 10
+        !params.containsKey('alpha-beta')
+
+        when:
+        params = [:]
+        CmdRun.addParam0(params, 'aaa-bbb-ccc', 1)
+        CmdRun.addParam0(params, 'aaaBbbCcc', 10)
+        then:
+        params['aaaBbbCcc'] == 10
+        !params.containsKey('aaa-bbb-ccc')
+
+    }
+
+    def 'should convert kebab case to camel case' () {
+
+        expect:
+        CmdRun.kebabToCamelCase('a') == 'a'
+        CmdRun.kebabToCamelCase('A') == 'A'
+        CmdRun.kebabToCamelCase('a-b-c-') == 'aBC'
+        CmdRun.kebabToCamelCase('aa-bb-cc') == 'aaBbCc'
+        CmdRun.kebabToCamelCase('alpha-beta-delta') == 'alphaBetaDelta'
+        CmdRun.kebabToCamelCase('Alpha-Beta-delta') == 'AlphaBetaDelta'
+    }
 
     @Unroll
     def 'should check run name #STR' () {
@@ -392,4 +423,55 @@ class CmdRunTest extends Specification {
         and:
         !warning
     }
+
+    @Unroll
+    def 'should detect moduleBinaries' () {
+        given:
+        NextflowMeta.instance.moduleBinaries(INITIAL)
+        CmdRun.detectModuleBinaryFeature(new ConfigMap(CONFIG))
+
+        expect:
+        NextflowMeta.instance.isModuleBinariesEnabled() == EXPECTED
+
+        cleanup:
+        NextflowMeta.instance.moduleBinaries(false)
+
+        where:
+        INITIAL | CONFIG                                          | EXPECTED
+        true    | [nextflow: [enable: [ moduleBinaries: true ]]]  | true
+        false   | [nextflow: [enable: [ moduleBinaries: true ]]]  | true
+        false   | [nextflow: [enable: [ moduleBinaries: false ]]] | false
+        true    | [nextflow: [enable: [ moduleBinaries: false ]]] | true
+        false   | [:]                                             | false
+        true    | [:]                                             | true
+    }
+
+    @Unroll
+    def 'should detect strict mode' () {
+        given:
+        NextflowMeta.instance.strictMode(INITIAL)
+        CmdRun.detectStrictFeature(new ConfigMap(CONFIG), ENV)
+
+        expect:
+        NextflowMeta.instance.isStrictModeEnabled() == EXPECTED
+
+        cleanup:
+        NextflowMeta.instance.strictMode(false)
+
+        where:
+        INITIAL | CONFIG                                  | ENV                        | EXPECTED
+        true    | [nextflow: [enable: [ strict: true ]]]  | [:]                        | true
+        false   | [nextflow: [enable: [ strict: true ]]]  | [:]                        | true
+        false   | [nextflow: [enable: [ strict: false ]]] | [:]                        | false
+        true    | [nextflow: [enable: [ strict: false ]]] | [:]                        | true
+        false   | [:]                                     | [:]                        | false
+        true    | [:]                                     | [:]                        | true
+        true    | [nextflow: [enable: [ strict: true ]]]  | [NXF_ENABLE_STRICT: true ] | true
+        false   | [nextflow: [enable: [ strict: true ]]]  | [NXF_ENABLE_STRICT: true ] | true
+        false   | [nextflow: [enable: [ strict: false ]]] | [NXF_ENABLE_STRICT: true ] | false
+        true    | [nextflow: [enable: [ strict: false ]]] | [NXF_ENABLE_STRICT: true ] | true
+        false   | [:]                                     | [NXF_ENABLE_STRICT: true ] | true
+        true    | [:]                                     | [NXF_ENABLE_STRICT: true ] | true
+
+    }
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/conda/CondaCacheTest.groovy b/modules/nextflow/src/test/groovy/nextflow/conda/CondaCacheTest.groovy
index 9e1f0c5ad4..f6b7fac271 100644
--- a/modules/nextflow/src/test/groovy/nextflow/conda/CondaCacheTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/conda/CondaCacheTest.groovy
@@ -89,6 +89,7 @@ class CondaCacheTest extends Specification {
         def cache = Spy(CondaCache)
         def BASE = Paths.get('/conda/envs')
         def ENV = folder.resolve('foo.yml')
+        def hash = CondaCache.sipHash(ENV)
         ENV.text = '''
             channels:
               - bioconda
@@ -99,13 +100,12 @@ class CondaCacheTest extends Specification {
               - bwa=0.7.15        
             '''
             .stripIndent(true)  // https://issues.apache.org/jira/browse/GROOVY-9423
-
         when:
         def prefix = cache.condaPrefixPath(ENV.toString())
         then:
         1 * cache.isYamlFilePath(ENV.toString())
         1 * cache.getCacheDir() >> BASE
-        prefix.toString() == '/conda/envs/foo-9416240708c49c4e627414b46a743664'
+        prefix.toString() == "/conda/envs/env-${hash}-9416240708c49c4e627414b46a743664"
 
         cleanup:
         folder?.deleteDir()
@@ -118,6 +118,7 @@ class CondaCacheTest extends Specification {
         def cache = Spy(CondaCache)
         def BASE = Paths.get('/conda/envs')
         def ENV = Files.createTempFile('test','.yml')
+        def hash = CondaCache.sipHash(ENV)
         ENV.text = '''  
             name: my-env-1.1
             channels:
@@ -135,7 +136,7 @@ class CondaCacheTest extends Specification {
         then:
         1 * cache.isYamlFilePath(ENV.toString())
         1 * cache.getCacheDir() >> BASE
-        prefix.toString() == '/conda/envs/my-env-1.1-e7fafe40ca966397a2c0d9bed7181aa7'
+        prefix.toString() == "/conda/envs/env-${hash}-e7fafe40ca966397a2c0d9bed7181aa7"
 
     }
 
@@ -146,6 +147,7 @@ class CondaCacheTest extends Specification {
         def cache = Spy(CondaCache)
         def BASE = Paths.get('/conda/envs')
         def ENV = folder.resolve('bar.txt')
+        def hash = CondaCache.sipHash(ENV)
         ENV.text = '''
                 star=2.5.4a
                 bwa=0.7.15   
@@ -159,7 +161,7 @@ class CondaCacheTest extends Specification {
         1 * cache.isYamlFilePath(ENV.toString())
         1 * cache.isTextFilePath(ENV.toString())
         1 * cache.getCacheDir() >> BASE
-        prefix.toString() == '/conda/envs/bar-8a4aa7db8ddb8ce4eb4d450d4814a437'
+        prefix.toString() == "/conda/envs/env-${hash}-8a4aa7db8ddb8ce4eb4d450d4814a437"
 
         cleanup:
         folder?.deleteDir()
@@ -195,9 +197,8 @@ class CondaCacheTest extends Specification {
 
         when:
         // the prefix directory exists ==> no conda command is executed
-        def result = cache.createLocalCondaEnv(ENV)
+        def result = cache.createLocalCondaEnv(ENV, PREFIX)
         then:
-        1 * cache.condaPrefixPath(ENV) >> PREFIX
         0 * cache.isYamlFilePath(ENV)
         0 * cache.runCommand(_)
         result == PREFIX
@@ -222,9 +223,8 @@ class CondaCacheTest extends Specification {
 
         when:
         // the prefix directory exists ==> no mamba command is executed
-        def result = cache.createLocalCondaEnv(ENV)
+        def result = cache.createLocalCondaEnv(ENV, PREFIX)
         then:
-        1 * cache.condaPrefixPath(ENV) >> PREFIX
         0 * cache.isYamlFilePath(ENV)
         0 * cache.runCommand(_)
         result == PREFIX
@@ -240,6 +240,32 @@ class CondaCacheTest extends Specification {
 
     }
 
+    def 'should create a conda environment - using micromamba' () {
+
+        given:
+        def ENV = 'bwa=1.1.1'
+        def PREFIX = Files.createTempDirectory('foo')
+        def cache = Spy(new CondaCache(useMicromamba: true))
+
+        when:
+        // the prefix directory exists ==> no mamba command is executed
+        def result = cache.createLocalCondaEnv(ENV, PREFIX)
+        then:
+        0 * cache.isYamlFilePath(ENV)
+        0 * cache.runCommand(_)
+        result == PREFIX
+
+        when:
+        PREFIX.deleteDir()
+        result = cache.createLocalCondaEnv0(ENV, PREFIX)
+        then:
+        1 * cache.isYamlFilePath(ENV)
+        0 * cache.makeAbsolute(_)
+        1 * cache.runCommand("micromamba create --yes --quiet --prefix $PREFIX $ENV") >> null
+        result == PREFIX
+
+    }
+
     def 'should create a conda environment using mamba and remote lock file' () {
 
         given:
@@ -249,9 +275,8 @@ class CondaCacheTest extends Specification {
 
         when:
         // the prefix directory exists ==> no mamba command is executed
-        def result = cache.createLocalCondaEnv(ENV)
+        def result = cache.createLocalCondaEnv(ENV, PREFIX)
         then:
-        1 * cache.condaPrefixPath(ENV) >> PREFIX
         0 * cache.isYamlFilePath(ENV)
         0 * cache.runCommand(_)
         result == PREFIX
@@ -265,6 +290,31 @@ class CondaCacheTest extends Specification {
         1 * cache.runCommand("mamba env create --prefix $PREFIX --file $ENV") >> null
         result == PREFIX
 
+    }
+    def 'should create a conda environment using micromamba and remote lock file' () {
+
+        given:
+        def ENV = 'http://foo.com/some/file-lock.yml'
+        def PREFIX = Files.createTempDirectory('foo')
+        def cache = Spy(new CondaCache(useMicromamba: true))
+
+        when:
+        // the prefix directory exists ==> no mamba command is executed
+        def result = cache.createLocalCondaEnv(ENV, PREFIX)
+        then:
+        0 * cache.isYamlFilePath(ENV)
+        0 * cache.runCommand(_)
+        result == PREFIX
+
+        when:
+        PREFIX.deleteDir()
+        result = cache.createLocalCondaEnv0(ENV, PREFIX)
+        then:
+        1 * cache.isYamlFilePath(ENV)
+        0 * cache.makeAbsolute(_)
+        1 * cache.runCommand("micromamba env create --yes --prefix $PREFIX --file $ENV") >> null
+        result == PREFIX
+
     }
 
     def 'should create conda env with options' () {
@@ -301,6 +351,23 @@ class CondaCacheTest extends Specification {
         result == PREFIX
     }
 
+    def 'should create conda env with options - using micromamba' () {
+        given:
+        def ENV = 'bwa=1.1.1'
+        def PREFIX = Paths.get('/foo/bar')
+        and:
+        def cache = Spy(new CondaCache(useMicromamba: true, createOptions: '--this --that'))
+
+        when:
+        def result = cache.createLocalCondaEnv0(ENV, PREFIX)
+        then:
+        1 * cache.isYamlFilePath(ENV)
+        1 * cache.isTextFilePath(ENV)
+        0 * cache.makeAbsolute(_)
+        1 * cache.runCommand("micromamba create --this --that --yes --quiet --prefix $PREFIX $ENV") >> null
+        result == PREFIX
+    }
+
     def 'should create conda env with channels' () {
         given:
         def ENV = 'bwa=1.1.1'
@@ -336,6 +403,24 @@ class CondaCacheTest extends Specification {
 
     }
 
+    def 'should create a conda env with a yaml file - using micromamba' () {
+
+        given:
+        def ENV = 'foo.yml'
+        def PREFIX = Paths.get('/conda/envs/my-env')
+        def cache = Spy(new CondaCache(useMicromamba: true))
+
+        when:
+        def result = cache.createLocalCondaEnv0(ENV, PREFIX)
+        then:
+        1 * cache.isYamlFilePath(ENV)
+        0 * cache.isTextFilePath(ENV)
+        1 * cache.makeAbsolute(ENV) >> Paths.get('/usr/base').resolve(ENV)
+        1 * cache.runCommand( "micromamba env create --yes --prefix $PREFIX --file /usr/base/foo.yml" ) >> null
+        result == PREFIX
+
+    }
+
     def 'should create a conda env with a text file' () {
 
         given:
@@ -355,6 +440,25 @@ class CondaCacheTest extends Specification {
 
     }
 
+    def 'should create a conda env with a text file - using micromamba' () {
+
+        given:
+        def ENV = 'foo.txt'
+        def PREFIX = Paths.get('/conda/envs/my-env')
+        and:
+        def cache = Spy(new CondaCache(useMicromamba: true, createOptions: '--this --that'))
+
+        when:
+        def result = cache.createLocalCondaEnv0(ENV, PREFIX)
+        then:
+        1 * cache.isYamlFilePath(ENV)
+        1 * cache.isTextFilePath(ENV)
+        1 * cache.makeAbsolute(ENV) >> Paths.get('/usr/base').resolve(ENV)
+        1 * cache.runCommand( "micromamba create --this --that --yes --quiet --prefix $PREFIX --file /usr/base/foo.txt" ) >> null
+        result == PREFIX
+
+    }
+
     def 'should get options from the config' () {
 
         when:
diff --git a/modules/nextflow/src/test/groovy/nextflow/config/ConfigParserTest.groovy b/modules/nextflow/src/test/groovy/nextflow/config/ConfigParserTest.groovy
index ebe6f02e47..a128f0fd36 100644
--- a/modules/nextflow/src/test/groovy/nextflow/config/ConfigParserTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/config/ConfigParserTest.groovy
@@ -16,8 +16,6 @@
 
 package nextflow.config
 
-import spock.lang.Ignore
-
 import java.nio.file.Files
 import java.nio.file.NoSuchFileException
 import java.nio.file.Path
@@ -26,11 +24,12 @@ import com.sun.net.httpserver.Headers
 import com.sun.net.httpserver.HttpExchange
 import com.sun.net.httpserver.HttpHandler
 import com.sun.net.httpserver.HttpServer
+import nextflow.SysEnv
 import nextflow.exception.ConfigParseException
-import spock.lang.Specification
-
 import nextflow.util.Duration
 import nextflow.util.MemoryUnit
+import spock.lang.Ignore
+import spock.lang.Specification
 
 /**
  *
@@ -38,6 +37,23 @@ import nextflow.util.MemoryUnit
  */
 class ConfigParserTest extends Specification {
 
+    def 'should get an environment variable' () {
+        given:
+        SysEnv.push(MAX_CPUS: '1')
+
+        when:
+        def CONFIG = '''
+        process.cpus = env('MAX_CPUS')
+        '''
+        def config = new ConfigParser().parse(CONFIG)
+
+        then:
+        config.process.cpus == '1'
+
+        cleanup:
+        SysEnv.pop()
+    }
+
     def 'should parse plugins id' () {
         given:
         def CONFIG = '''
diff --git a/modules/nextflow/src/test/groovy/nextflow/config/ManifestTest.groovy b/modules/nextflow/src/test/groovy/nextflow/config/ManifestTest.groovy
index d189b28f28..2860cb3c3e 100644
--- a/modules/nextflow/src/test/groovy/nextflow/config/ManifestTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/config/ManifestTest.groovy
@@ -16,7 +16,10 @@
 
 package nextflow.config
 
+import nextflow.exception.AbortOperationException
 import spock.lang.Specification
+
+import static nextflow.config.Manifest.ContributionType
 /**
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
@@ -26,38 +29,126 @@ class ManifestTest extends Specification {
     def 'should check manifest object' () {
 
         given:
-        def MAN = [author: 'pablo', nextflowVersion: '1.2.3', name: 'foo']
-
+        def MAP = [
+            author: 'pablo',
+            contributors: [
+                [
+                    name: 'Alice', 
+                    affiliation: 'University', 
+                    email: 'alice@university.edu',
+                    contribution: ['author', 'maintainer'],
+                    orcid: 'https://orcid.org/0000-0000-0000-0000'
+                ],
+                [
+                    name: 'Bob', 
+                    affiliation: 'Company', 
+                    email: 'bob@company.com',
+                    contribution: ['contributor'],
+                ]
+            ],
+            nextflowVersion: '1.2.3',
+            name: 'foo',
+            organization: 'My Organization',
+            icon: 'icon.png',
+            docsUrl: 'https://docs.io',
+            license: 'Apache v2'
+        ]
         when:
-        def manifest = new Manifest(MAN)
+        def manifest = new Manifest(MAP)
         then:
-        manifest.with {
-            author == 'pablo'
-            nextflowVersion == '1.2.3'
-            name == 'foo'
-        }
+        manifest.author == 'pablo'
+        manifest.contributors.size() == 2
+        manifest.contributors[0].name == 'Alice'
+        manifest.contributors[0].affiliation == 'University'
+        manifest.contributors[0].email == 'alice@university.edu'
+        manifest.contributors[0].contribution == [ContributionType.AUTHOR, ContributionType.MAINTAINER] as Set
+        manifest.contributors[0].orcid == 'https://orcid.org/0000-0000-0000-0000'
+        manifest.contributors[1].name == 'Bob'
+        manifest.contributors[1].affiliation == 'Company'
+        manifest.contributors[1].email == 'bob@company.com'
+        manifest.contributors[1].contribution == [ContributionType.CONTRIBUTOR] as Set
+        manifest.nextflowVersion == '1.2.3'
+        manifest.name == 'foo'
+        manifest.organization == 'My Organization'
+        manifest.icon == 'icon.png'
+        manifest.docsUrl == 'https://docs.io'
+        manifest.license == 'Apache v2'
 
     }
 
     def 'should check empty manifest' () {
 
-        // check empty manifest
         when:
         def manifest = new Manifest(new ConfigObject())
         then:
-        manifest.with {
-            homePage == null
-            defaultBranch == 'master'
-            description == null
-            author == null
-            mainScript == 'main.nf'
-            gitmodules == null
-            nextflowVersion == null
-            version == null
-            name == null
-        }
+        manifest.homePage == null
+        manifest.defaultBranch == null
+        manifest.description == null
+        manifest.author == null
+        manifest.contributors == []
+        manifest.mainScript == 'main.nf'
+        manifest.gitmodules == null
+        manifest.nextflowVersion == null
+        manifest.version == null
+        manifest.name == null
+        manifest.docsUrl == null
+        manifest.organization == null
+        manifest.icon == null
+        manifest.license == null
+
+    }
 
+    def 'should convert manifest to map' () {
+
+        when:
+        def MAP = [
+            name: 'Alice', 
+            affiliation: 'University', 
+            email: 'alice@university.edu',
+            contribution: ['author', 'maintainer'],
+            orcid: 'https://orcid.org/0000-0000-0000-0000'
+        ]
+        then:
+        new Manifest.Contributor(MAP).toMap() == [
+            name: 'Alice', 
+            affiliation: 'University', 
+            email: 'alice@university.edu',
+            github: null,
+            contribution: ['author', 'maintainer'],
+            orcid: 'https://orcid.org/0000-0000-0000-0000'
+        ]
     }
 
+    def 'should throw error on invalid manifest' () {
+        when:
+        def manifest = new Manifest([
+            contributors: [ 'Alice' ]
+        ])
+        manifest.contributors
+        then:
+        thrown(AbortOperationException)
+
+        when:
+        manifest = new Manifest([
+            contributors: [[
+                name: 'Alice',
+                contribution: 'author'
+            ]]
+        ])
+        manifest.contributors
+        then:
+        thrown(AbortOperationException)
+
+        when:
+        manifest = new Manifest([
+            contributors: [[
+                name: 'Alice',
+                contribution: [ 'owner' ]
+            ]]
+        ])
+        manifest.contributors
+        then:
+        thrown(AbortOperationException)
+    }
 
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/CharliecloudBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/CharliecloudBuilderTest.groovy
index 896f7a71c0..ba8e1b77bb 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/CharliecloudBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/CharliecloudBuilderTest.groovy
@@ -36,102 +36,124 @@ class CharliecloudBuilderTest extends Specification {
         def path2 = Paths.get('/bar/data/file2')
 
         expect:
-        new CharliecloudBuilder('/cacheDir/img/busybox')
+        new CharliecloudBuilder('/cacheDir/busybox')
                 .build()
-                .runCommand == 'ch-convert -i ch-image --storage /cacheDir busybox "$NXF_TASK_WORKDIR"/container_busybox && ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w -b "$NXF_TASK_WORKDIR" "$NXF_TASK_WORKDIR"/container_busybox --'
+                .runCommand == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env --write-fake -b "$NXF_TASK_WORKDIR" /cacheDir/busybox --'
 
-        new CharliecloudBuilder('/cacheDir/img/busybox')
+        new CharliecloudBuilder('/cacheDir/busybox')
+                .params(writeFake: false)
+                .build()
+                .runCommand == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w -b "$NXF_TASK_WORKDIR" /cacheDir/busybox --'
+
+        new CharliecloudBuilder('/cacheDir/busybox')
+                .params(writeFake: false)
+                .params(readOnlyInputs: true)
+                .build()
+                .runCommand == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -b "$NXF_TASK_WORKDIR" /cacheDir/busybox --'
+
+        new CharliecloudBuilder('/cacheDir/busybox')
                 .params(runOptions: '-j --no-home')
                 .build()
-                .runCommand == 'ch-convert -i ch-image --storage /cacheDir busybox "$NXF_TASK_WORKDIR"/container_busybox && ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w -b "$NXF_TASK_WORKDIR" -j --no-home "$NXF_TASK_WORKDIR"/container_busybox --'
+                .runCommand == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env --write-fake -b "$NXF_TASK_WORKDIR" -j --no-home /cacheDir/busybox --'
         
-        new CharliecloudBuilder('/cacheDir/img/busybox')
+        new CharliecloudBuilder('/cacheDir/busybox')
                 .params(temp: '/foo')
                 .build()
-                .runCommand == 'ch-convert -i ch-image --storage /cacheDir busybox "$NXF_TASK_WORKDIR"/container_busybox && ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w -b /foo:/tmp -b "$NXF_TASK_WORKDIR" "$NXF_TASK_WORKDIR"/container_busybox --'
+                .runCommand == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env --write-fake -b /foo:/tmp -b "$NXF_TASK_WORKDIR" /cacheDir/busybox --'
 
-        new CharliecloudBuilder('/cacheDir/img/busybox')
+        new CharliecloudBuilder('/cacheDir/busybox')
                 .addEnv('X=1')
                 .addEnv(ALPHA:'aaa', BETA: 'bbb')
                 .build()
-                .runCommand == 'ch-convert -i ch-image --storage /cacheDir busybox "$NXF_TASK_WORKDIR"/container_busybox && ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w --set-env=X=1 --set-env=ALPHA=aaa --set-env=BETA=bbb -b "$NXF_TASK_WORKDIR" "$NXF_TASK_WORKDIR"/container_busybox --'
+                .runCommand == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env --write-fake --set-env=X=1 --set-env=ALPHA=aaa --set-env=BETA=bbb -b "$NXF_TASK_WORKDIR" /cacheDir/busybox --'
 
-        new CharliecloudBuilder('/cacheDir/img/ubuntu')
+        new CharliecloudBuilder('/cacheDir/ubuntu')
                 .addMount(path1)
                 .build()
-                .runCommand == 'ch-convert -i ch-image --storage /cacheDir ubuntu "$NXF_TASK_WORKDIR"/container_ubuntu && ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w -b /foo/data/file1 -b "$NXF_TASK_WORKDIR" "$NXF_TASK_WORKDIR"/container_ubuntu --'
+                .runCommand == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env --write-fake -b /foo/data/file1 -b "$NXF_TASK_WORKDIR" /cacheDir/ubuntu --'
 
-        new CharliecloudBuilder('/cacheDir/img/ubuntu')
+        new CharliecloudBuilder('/cacheDir/ubuntu')
                 .addMount(path1)
                 .addMount(path2)
                 .build()
-                .runCommand == 'ch-convert -i ch-image --storage /cacheDir ubuntu "$NXF_TASK_WORKDIR"/container_ubuntu && ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w -b /foo/data/file1 -b /bar/data/file2 -b "$NXF_TASK_WORKDIR" "$NXF_TASK_WORKDIR"/container_ubuntu --'
+                .runCommand == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env --write-fake -b /foo/data/file1 -b /bar/data/file2 -b "$NXF_TASK_WORKDIR" /cacheDir/ubuntu --'
     }
 
     def db_file = Paths.get('/home/db')
     def 'should get run command' () {
 
         when:
-        def cmd = new CharliecloudBuilder('/cacheDir/img/ubuntu')
+        def cmd = new CharliecloudBuilder('/cacheDir/ubuntu')
             .build()
             .getRunCommand()
         then:
-        cmd == 'ch-convert -i ch-image --storage /cacheDir ubuntu "$NXF_TASK_WORKDIR"/container_ubuntu && ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w -b "$NXF_TASK_WORKDIR" "$NXF_TASK_WORKDIR"/container_ubuntu --'
+        cmd == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env --write-fake -b "$NXF_TASK_WORKDIR" /cacheDir/ubuntu --'
 
         when:
-        cmd = new CharliecloudBuilder('/cacheDir/img/ubuntu')
-            .params(useSquash: 'true')
+        cmd = new CharliecloudBuilder('/cacheDir/ubuntu')
+            .params(writeFake: 'true')
             .build()
             .getRunCommand()
         then:
-        cmd == 'ch-convert -i ch-image --storage /cacheDir ubuntu "$NXF_TASK_WORKDIR"/container_ubuntu.squashfs && ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w -b "$NXF_TASK_WORKDIR" "$NXF_TASK_WORKDIR"/container_ubuntu.squashfs --'
+        cmd == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env --write-fake -b "$NXF_TASK_WORKDIR" /cacheDir/ubuntu --'
 
         when:
-        cmd = new CharliecloudBuilder('/cacheDir/img/ubuntu')
-            .params(writeFake: 'true')
+        cmd = new CharliecloudBuilder('/cacheDir/ubuntu')
+            .params(writeFake: 'false')
             .build()
             .getRunCommand()
         then:
-        cmd == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env --write-fake -w -b "$NXF_TASK_WORKDIR" ubuntu --'
+        cmd == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w -b "$NXF_TASK_WORKDIR" /cacheDir/ubuntu --'
 
         when:
-        cmd = new CharliecloudBuilder('/cacheDir/img/ubuntu')
+        cmd = new CharliecloudBuilder('/cacheDir/ubuntu')
             .params(entry:'/bin/sh')
             .build()
             .getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'ch-convert -i ch-image --storage /cacheDir ubuntu "$NXF_TASK_WORKDIR"/container_ubuntu && ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w -b "$NXF_TASK_WORKDIR" "$NXF_TASK_WORKDIR"/container_ubuntu -- /bin/sh -c "bwa --this --that file.fastq"'
+        cmd == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env --write-fake -b "$NXF_TASK_WORKDIR" /cacheDir/ubuntu -- /bin/sh -c "bwa --this --that file.fastq"'
 
         when:
-        cmd = new CharliecloudBuilder('/cacheDir/img/ubuntu')
+        cmd = new CharliecloudBuilder('/cacheDir/ubuntu')
             .params(entry:'/bin/sh')
             .params(readOnlyInputs: 'true')
             .build()
             .getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'ch-convert -i ch-image --storage /cacheDir ubuntu "$NXF_TASK_WORKDIR"/container_ubuntu && ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -b "$NXF_TASK_WORKDIR" "$NXF_TASK_WORKDIR"/container_ubuntu -- /bin/sh -c "bwa --this --that file.fastq"'
+        cmd == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env --write-fake -b "$NXF_TASK_WORKDIR" /cacheDir/ubuntu -- /bin/sh -c "bwa --this --that file.fastq"'
 
         when:
-        cmd = new CharliecloudBuilder('/cacheDir/img/ubuntu')
+        cmd = new CharliecloudBuilder('/cacheDir/ubuntu')
             .params(entry:'/bin/sh')
             .params(readOnlyInputs: 'false')
             .build()
             .getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'ch-convert -i ch-image --storage /cacheDir ubuntu "$NXF_TASK_WORKDIR"/container_ubuntu && ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w -b "$NXF_TASK_WORKDIR" "$NXF_TASK_WORKDIR"/container_ubuntu -- /bin/sh -c "bwa --this --that file.fastq"'
+        cmd == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env --write-fake -b "$NXF_TASK_WORKDIR" /cacheDir/ubuntu -- /bin/sh -c "bwa --this --that file.fastq"'
 
         when:
-        cmd = new CharliecloudBuilder('/cacheDir/img/ubuntu')
+        cmd = new CharliecloudBuilder('/cacheDir/ubuntu')
             .params(entry:'/bin/sh')
+            .params(readOnlyInputs: 'false')
+            .params(writeFake: 'false')
+            .build()
+            .getRunCommand('bwa --this --that file.fastq')
+        then:
+        cmd == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w -b "$NXF_TASK_WORKDIR" /cacheDir/ubuntu -- /bin/sh -c "bwa --this --that file.fastq"'
+
+        when:
+        cmd = new CharliecloudBuilder('/cacheDir/ubuntu')
+            .params(entry:'/bin/sh')
+            .params(readOnlyInputs: 'true')
+            .params(writeFake: 'false')
             .addMount(db_file)
             .addMount(db_file)
-            .params(readOnlyInputs: 'true')
             .build().getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'ch-convert -i ch-image --storage /cacheDir ubuntu "$NXF_TASK_WORKDIR"/container_ubuntu && ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -b /home -b "$NXF_TASK_WORKDIR" "$NXF_TASK_WORKDIR"/container_ubuntu -- /bin/sh -c "bwa --this --that file.fastq"'
+        cmd == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -b /home -b "$NXF_TASK_WORKDIR" /cacheDir/ubuntu -- /bin/sh -c "bwa --this --that file.fastq"'
 
         when:
-        cmd = new CharliecloudBuilder('/cacheDir/img/ubuntu')
+        cmd = new CharliecloudBuilder('/cacheDir/ubuntu')
             .params(entry:'/bin/sh')
             .addMount(db_file)
             .addMount(db_file)
@@ -139,7 +161,7 @@ class CharliecloudBuilderTest extends Specification {
             .build()
             .getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'ch-convert -i ch-image --storage /cacheDir ubuntu "$NXF_TASK_WORKDIR"/container_ubuntu && ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w -b /home/db -b "$NXF_TASK_WORKDIR" "$NXF_TASK_WORKDIR"/container_ubuntu -- /bin/sh -c "bwa --this --that file.fastq"'
+        cmd == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env --write-fake -b /home/db -b "$NXF_TASK_WORKDIR" /cacheDir/ubuntu -- /bin/sh -c "bwa --this --that file.fastq"'
     }
 
     @Unroll
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/CharliecloudCacheTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/CharliecloudCacheTest.groovy
index 5207af9a1a..2098526d82 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/CharliecloudCacheTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/CharliecloudCacheTest.groovy
@@ -47,7 +47,7 @@ class CharliecloudCacheTest extends Specification {
         'foo:bar'                   | 'foo+bar'
     }
 
-    def 'should return the cache dir from the config file' () {
+    def 'should return the cache dir from the config file'() {
 
         given:
         def dir = Files.createTempDirectory('test')
@@ -63,7 +63,7 @@ class CharliecloudCacheTest extends Specification {
         dir.deleteDir()
     }
 
-    def 'should return the cache dir from the environment' () {
+    def 'should return the cache dir from the environment'() {
 
         given:
         def dir = Files.createTempDirectory('test')
@@ -79,6 +79,84 @@ class CharliecloudCacheTest extends Specification {
         dir.deleteDir()
     }
 
+    def 'should use CH_IMAGE_STORAGE over cacheDir'() {
+
+        given:
+        def dir = Files.createTempDirectory('test')
+        and:
+        def cacheDir = dir.resolve('nxf.ch')
+        and:
+        def charliecloudCacheDir = dir.resolve('charliecloud')
+
+        when:
+        def cache = new CharliecloudCache([cacheDir: "$cacheDir"] as ContainerConfig, [CH_IMAGE_STORAGE: "$charliecloudCacheDir"])
+     
+        then:
+        cache.getCacheDir() == charliecloudCacheDir
+
+        cleanup:
+        dir.deleteDir()
+    }
+
+    def 'should use CH_IMAGE_STORAGE over NXF_CHARLIECLOUD_CACHEDIR'() {
+
+        given:
+        def dir = Files.createTempDirectory('test')
+        and:
+        def cacheDir = dir.resolve('nxf.ch')
+        and:
+        def charliecloudCacheDir = dir.resolve('charliecloud')
+
+        when:
+        def cache = new CharliecloudCache(GroovyMock(ContainerConfig), [NXF_CHARLIECLOUD_CACHEDIR: "$cacheDir", CH_IMAGE_STORAGE: "$charliecloudCacheDir"])
+     
+        then:
+        cache.getCacheDir() == charliecloudCacheDir
+
+        cleanup:
+        dir.deleteDir()
+    }
+
+    def 'should throw exception: cacheDir and CH_IMAGE_STORAGE are the same'() {
+
+        given:
+        def dir = Files.createTempDirectory('test')
+        and:
+        def cacheDir = dir.resolve('nxf.ch')
+
+        when:
+        def cache = new CharliecloudCache([cacheDir: "$cacheDir", writeFake: 'false'] as ContainerConfig, [CH_IMAGE_STORAGE: "$cacheDir"])
+        and:
+        cache.getCacheDir()
+
+        then:
+        def e = thrown(Exception)
+        e.message == "`charliecloud.cacheDir` configuration parameter must be different from env variable `CH_IMAGE_STORAGE`"
+
+        cleanup:
+        dir.deleteDir()
+    }
+
+    def 'should throw exception: NXF_CHARLIECLOUD_CACHEDIR and CH_IMAGE_STORAGE are the same'() {
+
+        given:
+        def dir = Files.createTempDirectory('test')
+        and:
+        def cacheDir = dir.resolve('nxf.ch')
+
+        when:
+        def cache = new CharliecloudCache([writeFake: 'false'] as ContainerConfig, [ NXF_CHARLIECLOUD_CACHEDIR: "$cacheDir", CH_IMAGE_STORAGE: "$cacheDir" ])
+        and:
+        cache.getCacheDir()
+        
+        then:
+        def e = thrown(Exception)
+        e.message == "`NXF_CHARLIECLOUD_CACHEDIR` env variable must be different from env variable `CH_IMAGE_STORAGE`"
+
+        cleanup:
+        dir.deleteDir()
+    }
+
     def 'should run ch-image pull command'() {
 
         given:
@@ -131,7 +209,7 @@ class CharliecloudCacheTest extends Specification {
 
     @Ignore
     @Timeout(1)
-    def 'should pull a charliecloud image' () {
+    def 'should pull a charliecloud image'() {
 
         given:
         def IMAGE = 'busybox:latest'
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/inspect/ContainersInspectorTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/inspect/ContainersInspectorTest.groovy
index 6cba96dd92..2da436e431 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/inspect/ContainersInspectorTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/inspect/ContainersInspectorTest.groovy
@@ -50,7 +50,7 @@ class ContainersInspectorTest extends Specification {
         ]
 
         when:
-        def observer = new ContainersInspector(dag)
+        def observer = new ContainersInspector(dag, false)
         then:
         observer.getContainers() == [
             'proc1': 'container1',
@@ -67,20 +67,20 @@ class ContainersInspectorTest extends Specification {
         ]
 
         when:
-        def result = new ContainersInspector(dag)
+        def result = new ContainersInspector(dag, false)
                 .withFormat('json')
                 .renderContainers()
         then:
         result == '''\
             {
                 "processes": [
-                    {
-                        "name": "proc2",
-                        "container": "container2"
-                    },
                     {
                         "name": "proc1",
                         "container": "container1"
+                    },
+                    {
+                        "name": "proc2",
+                        "container": "container2"
                     }
                 ]
             }
@@ -96,13 +96,13 @@ class ContainersInspectorTest extends Specification {
         ]
 
         when:
-        def result = new ContainersInspector(dag)
+        def result = new ContainersInspector(dag,false)
                 .withFormat('config')
                 .renderContainers()
         then:
         result == '''\
-            process { withName: 'proc2' { container = 'container2' } }
             process { withName: 'proc1' { container = 'container1' } }
+            process { withName: 'proc2' { container = 'container2' } }
             '''.stripIndent(true)
     }
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/datasource/SraExplorerTest.groovy b/modules/nextflow/src/test/groovy/nextflow/datasource/SraExplorerTest.groovy
index d251873a3a..acad4be7cb 100644
--- a/modules/nextflow/src/test/groovy/nextflow/datasource/SraExplorerTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/datasource/SraExplorerTest.groovy
@@ -16,6 +16,8 @@
 
 package nextflow.datasource
 
+import dev.failsafe.FailsafeException
+
 import java.nio.file.Files
 import java.nio.file.Path
 
@@ -242,4 +244,35 @@ class SraExplorerTest extends Specification {
         result == '1bc'
     }
 
+    def 'should detect retry errors' () {
+        given:
+            def ex = new IOException("Server returned HTTP response code: " + ERROR +" for URL: https://dummy.url")
+
+        expect:
+            SraExplorer.containsErrorCodes(ex.getLocalizedMessage(), SraExplorer.RETRY_CODES) == EXPECTED
+
+        where:
+            ERROR | EXPECTED
+            '404'   | false
+            '429'   | true
+
+    }
+    def 'should retry on errors' () {
+        given:
+        def ex = new IOException("Server returned HTTP response code: 429 for URL: https://dummy.url")
+        def slurper = new SraExplorer(null, [retryPolicy: [maxAttempts: 2]])
+        def retries = 0
+
+        when:
+        slurper.runWithRetry{
+                retries ++
+                throw ex
+        }
+
+        then:
+        def e = thrown(FailsafeException)
+        e.cause.message == ex.message
+        retries == 2
+    }
+
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/datasource/SraRetryConfigTest.groovy b/modules/nextflow/src/test/groovy/nextflow/datasource/SraRetryConfigTest.groovy
new file mode 100644
index 0000000000..61fc9c1339
--- /dev/null
+++ b/modules/nextflow/src/test/groovy/nextflow/datasource/SraRetryConfigTest.groovy
@@ -0,0 +1,44 @@
+/*
+ * Copyright 2013-2024, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.datasource
+
+import nextflow.util.Duration
+import spock.lang.Specification
+
+/**
+ *
+ * @author Jorge Ejarque <jorge.ejarque@seqera.io>
+ */
+class SraRetryConfigTest extends Specification {
+
+    def 'should create retry config'() {
+
+        expect:
+        new SraRetryConfig().delay == Duration.of('500ms')
+        new SraRetryConfig().maxDelay == Duration.of('30s')
+        new SraRetryConfig().maxAttempts == 3
+        new SraRetryConfig().jitter == 0.25d
+
+        and:
+        new SraRetryConfig([maxAttempts: 20]).maxAttempts == 20
+        new SraRetryConfig([delay: '1s']).delay == Duration.of('1s')
+        new SraRetryConfig([maxDelay: '1m']).maxDelay == Duration.of('1m')
+        new SraRetryConfig([jitter: '0.5']).jitter == 0.5d
+
+    }
+}
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/AbstractGridExecutorTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/AbstractGridExecutorTest.groovy
index 244f26c359..8269e89077 100644
--- a/modules/nextflow/src/test/groovy/nextflow/executor/AbstractGridExecutorTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/executor/AbstractGridExecutorTest.groovy
@@ -32,11 +32,11 @@ class AbstractGridExecutorTest extends Specification {
     def 'should remove invalid chars from name' () {
 
         given:
-        def task = new TaskRun(name: 'task 90 (foo:bar/baz)')
+        def task = new TaskRun(name: 'task 90 = (foo:bar/baz)')
         def exec = [:] as AbstractGridExecutor
 
         expect:
-        exec.getJobNameFor(task) == 'nf-task_90_(foo_bar_baz)'
+        exec.getJobNameFor(task) == 'nf-task_90___(foo_bar_baz)'
 
     }
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
index e301a376c8..3b93c4c360 100644
--- a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
@@ -559,7 +559,7 @@ class BashWrapperBuilderTest extends Specification {
         binding.unstage_outputs == '''\
                 IFS=$'\\n'
                 for name in $(eval "ls -1d test.bam test.bai" | sort | uniq); do
-                    nxf_fs_copy "$name" /work/dir || true
+                    nxf_fs_copy "$name" /work/dir
                 done
                 unset IFS
                 '''.stripIndent().rightTrim()
@@ -576,7 +576,7 @@ class BashWrapperBuilderTest extends Specification {
         binding.unstage_outputs == '''\
                 IFS=$'\\n'
                 for name in $(eval "ls -1d test.bam test.bai" | sort | uniq); do
-                    nxf_fs_move "$name" /another/dir || true
+                    nxf_fs_move "$name" /another/dir
                 done
                 unset IFS
                 '''.stripIndent().rightTrim()
@@ -781,7 +781,24 @@ class BashWrapperBuilderTest extends Specification {
                 # conda environment
                 source $(conda info --json | awk '/conda_prefix/ { gsub(/"|,/, "", $2); print $2 }')/bin/activate /some/conda/env/foo
                 '''.stripIndent()
+    }
+
+    def 'should create micromamba activate snippet' () {
 
+        when:
+        def binding = newBashWrapperBuilder().makeBinding()
+        then:
+        binding.conda_activate == null
+        binding.containsKey('conda_activate')
+
+        when:
+        def CONDA = Paths.get('/some/conda/env/foo')
+        binding = newBashWrapperBuilder([condaEnv: CONDA, 'useMicromamba': true]).makeBinding()
+        then:
+        binding.conda_activate == '''\
+                # conda environment
+                eval "$(micromamba shell hook --shell bash)" && micromamba activate /some/conda/env/foo
+                '''.stripIndent()
     }
 
     def 'should create spack activate snippet' () {
@@ -1320,6 +1337,46 @@ class BashWrapperBuilderTest extends Specification {
         
     }
 
+    def 'should get unstage control script'(){
+        given:
+        BashWrapperBuilder builder
+        when:
+        builder = newBashWrapperBuilder()
+        then:
+        builder.getUnstageControls() == '''\
+                cp .command.out /work/dir/.command.out || true
+                cp .command.err /work/dir/.command.err || true
+                '''.stripIndent()
+
+
+        when:
+        builder = newBashWrapperBuilder(statsEnabled: true)
+        then:
+        builder.getUnstageControls() == '''\
+                cp .command.out /work/dir/.command.out || true
+                cp .command.err /work/dir/.command.err || true
+                cp .command.trace /work/dir/.command.trace || true
+                '''.stripIndent()
+
+        when:
+        builder = newBashWrapperBuilder(outputEnvNames: ['some-data'])
+        then:
+        builder.getUnstageControls() == '''\
+                cp .command.out /work/dir/.command.out || true
+                cp .command.err /work/dir/.command.err || true
+                cp .command.env /work/dir/.command.env || true
+                '''.stripIndent()
+
+        when:
+        builder = newBashWrapperBuilder(outputEvals: [some:'data'])
+        then:
+        builder.getUnstageControls() == '''\
+                cp .command.out /work/dir/.command.out || true
+                cp .command.err /work/dir/.command.err || true
+                cp .command.env /work/dir/.command.env || true
+                '''.stripIndent()
+    }
+
 
     def 'should create wrapper with podman' () {
         when:
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/FluxExecutorTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/FluxExecutorTest.groovy
index 3cc3a73396..95a90e65bc 100644
--- a/modules/nextflow/src/test/groovy/nextflow/executor/FluxExecutorTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/executor/FluxExecutorTest.groovy
@@ -72,27 +72,27 @@ class FluxExecutorTest extends Specification {
         then:
         // Flux doesn't have script headers
         executor.getHeaders(task) == ''
-        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'mini', 'submit', '--setattr=cwd=/work/path', '--job-name="nf-my_task"', '--output=/work/path/.command.log', '--queue=delta', '/bin/bash', 'job.sh']
+        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'submit', '--setattr=cwd=/work/path', '--job-name="nf-my_task"', '--output=/work/path/.command.log', '--queue=delta', '/bin/bash', 'job.sh']
 
         when:
         task.config = new TaskConfig()
         task.config.time = '1m'
         then:
-        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'mini', 'submit', '--setattr=cwd=/work/path', '--job-name="nf-my_task"', '--output=/work/path/.command.log', '--time-limit=01', '/bin/bash', 'job.sh']
+        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'submit', '--setattr=cwd=/work/path', '--job-name="nf-my_task"', '--output=/work/path/.command.log', '--time-limit=01', '/bin/bash', 'job.sh']
 
         when:
         task.config = new TaskConfig()
         task.config.time = '1h'
         task.config.clusterOptions = '--tasks-per-node=4'
         then:
-        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'mini', 'submit', '--setattr=cwd=/work/path', '--job-name="nf-my_task"', '--output=/work/path/.command.log', '--time-limit=60', '--tasks-per-node=4', '/bin/bash', 'job.sh']
+        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'submit', '--setattr=cwd=/work/path', '--job-name="nf-my_task"', '--output=/work/path/.command.log', '--time-limit=60', '--tasks-per-node=4', '/bin/bash', 'job.sh']
 
         when:
         task.config = new TaskConfig()
         task.config.time = '1h'
         task.config.clusterOptions = '--tasks-per-node=4 --cpus-per-node=4'
         then:
-        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'mini', 'submit', '--setattr=cwd=/work/path', '--job-name="nf-my_task"', '--output=/work/path/.command.log', '--time-limit=60', '--tasks-per-node=4', '--cpus-per-node=4', '/bin/bash', 'job.sh']
+        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'submit', '--setattr=cwd=/work/path', '--job-name="nf-my_task"', '--output=/work/path/.command.log', '--time-limit=60', '--tasks-per-node=4', '--cpus-per-node=4', '/bin/bash', 'job.sh']
 
     }
 
@@ -111,9 +111,9 @@ class FluxExecutorTest extends Specification {
         task.name = 'my task'
         task.workDir = Paths.get('/work/path')
         task.config = new TaskConfig()
-        
+
         expect:
-        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'mini', 'submit', '--setattr=cwd=/work/path', '--job-name="nf-my_task"', '/bin/bash', 'job.sh']
+        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'submit', '--setattr=cwd=/work/path', '--job-name="nf-my_task"', '/bin/bash', 'job.sh']
 
     }
 
@@ -135,7 +135,7 @@ class FluxExecutorTest extends Specification {
         task.index = 21
         task.config = new TaskConfig()
         then:
-        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'mini', 'submit', '--setattr=cwd="/work/some\\ data/path"', '--job-name="nf-my_task"', '--output="/work/some\\ data/path/.command.log"', '/bin/bash', 'job.sh']
+        executor.getSubmitCommandLine(task, Paths.get('/some/path/job.sh')) == ['flux', 'submit', '--setattr=cwd="/work/some\\ data/path"', '--job-name="nf-my_task"', '--output="/work/some\\ data/path/.command.log"', '/bin/bash', 'job.sh']
 
     }
 
@@ -160,8 +160,8 @@ class FluxExecutorTest extends Specification {
         result['ƒ6upwy2MY3'] == AbstractGridExecutor.QueueStatus.RUNNING
         result['ƒ6upcbFjvf'] == AbstractGridExecutor.QueueStatus.HOLD
         result['ƒ6uon2RGVV'] == AbstractGridExecutor.QueueStatus.PENDING
-        result['ƒ6upwy2MY4'] == AbstractGridExecutor.QueueStatus.DONE 
-        result['ƒ6upcbFjvh'] == AbstractGridExecutor.QueueStatus.DONE 
+        result['ƒ6upwy2MY4'] == AbstractGridExecutor.QueueStatus.DONE
+        result['ƒ6upcbFjvh'] == AbstractGridExecutor.QueueStatus.DONE
     }
 
     def testQueueStatusCommand() {
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/PbsExecutorTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/PbsExecutorTest.groovy
index b279c7eee2..174a7b3b12 100644
--- a/modules/nextflow/src/test/groovy/nextflow/executor/PbsExecutorTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/executor/PbsExecutorTest.groovy
@@ -172,7 +172,7 @@ class PbsExecutorTest extends Specification {
         }
         then:
         executor.getHeaders(taskArray) == '''
-                #PBS -J 0-4
+                #PBS -t 0-4
                 #PBS -N nf-task_name
                 #PBS -o /dev/null
                 #PBS -j oe
@@ -321,7 +321,7 @@ class PbsExecutorTest extends Specification {
         given:
         def executor = Spy(PbsExecutor)
         expect:
-        executor.getArrayIndexName() == 'PBS_ARRAY_INDEX'
+        executor.getArrayIndexName() == 'PBS_ARRAYID'
         executor.getArrayIndexStart() == 0
     }
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/SimpleFileCopyStrategyTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/SimpleFileCopyStrategyTest.groovy
index 29cbb35697..6361e4f394 100644
--- a/modules/nextflow/src/test/groovy/nextflow/executor/SimpleFileCopyStrategyTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/executor/SimpleFileCopyStrategyTest.groovy
@@ -270,7 +270,7 @@ class SimpleFileCopyStrategyTest extends Specification {
         script == '''
                 IFS=$'\\n'
                 for name in $(eval "ls -1d simple.txt my/path/file.bam" | sort | uniq); do
-                    nxf_fs_copy "$name" /target/work\\ dir || true
+                    nxf_fs_copy "$name" /target/work\\ dir
                 done
                 unset IFS
                 '''
@@ -293,7 +293,7 @@ class SimpleFileCopyStrategyTest extends Specification {
         script == '''
                 IFS=$'\\n'
                 for name in $(eval "ls -1d simple.txt my/path/file.bam" | sort | uniq); do
-                    nxf_fs_move "$name" /target/store || true
+                    nxf_fs_move "$name" /target/store
                 done
                 unset IFS
                 '''
@@ -315,7 +315,7 @@ class SimpleFileCopyStrategyTest extends Specification {
         script == '''
                 IFS=$'\\n'
                 for name in $(eval "ls -1d simple.txt my/path/file.bam" | sort | uniq); do
-                    nxf_fs_rsync "$name" /target/work\\'s || true
+                    nxf_fs_rsync "$name" /target/work\\'s
                 done
                 unset IFS
                 '''
diff --git a/modules/nextflow/src/test/groovy/nextflow/extension/JoinOpTest.groovy b/modules/nextflow/src/test/groovy/nextflow/extension/JoinOpTest.groovy
index 9893d9a797..673686fdf9 100644
--- a/modules/nextflow/src/test/groovy/nextflow/extension/JoinOpTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/extension/JoinOpTest.groovy
@@ -21,7 +21,9 @@ import nextflow.Channel
 import nextflow.Global
 import nextflow.Session
 import nextflow.exception.AbortOperationException
+import nextflow.util.ArrayBag
 import spock.lang.Specification
+
 /**
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
@@ -207,6 +209,35 @@ class JoinOpTest extends Specification {
 
     }
 
+    def 'should be able to use identical ArrayBags join key' () {
+        given:
+        def key1 = new ArrayBag(["key"])
+        def key2 = new ArrayBag(["key"])
+        def ch1 = Channel.of([key1, "foo"])
+        def ch2 = Channel.of([key2, "bar"])
+
+        when:
+        def op = new JoinOp(ch1 as DataflowReadChannel, ch2 as DataflowReadChannel)
+        List result = op.apply().toList().getVal()
+
+        then:
+        !result.isEmpty()
+    }
+
+    def 'should differentiate nonidentical ArrayBags join key' () {
+        given:
+        def key1 = new ArrayBag(["key", "key", "quay"])
+        def key2 = new ArrayBag(["quay", "quay", "key"])
+        def ch1 = Channel.of([key1, "foo"])
+        def ch2 = Channel.of([key2, "bar"])
+
+        when:
+        def op = new JoinOp(ch1 as DataflowReadChannel, ch2 as DataflowReadChannel)
+        List result = op.apply().toList().getVal()
+
+        then:
+        result.isEmpty()
+    }
 
     def 'should not fail on mismatches' () {
         given:
diff --git a/modules/nextflow/src/test/groovy/nextflow/processor/LocalPollingMonitorTest.groovy b/modules/nextflow/src/test/groovy/nextflow/processor/LocalPollingMonitorTest.groovy
index 54110fd475..e6f6150ce5 100644
--- a/modules/nextflow/src/test/groovy/nextflow/processor/LocalPollingMonitorTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/processor/LocalPollingMonitorTest.groovy
@@ -96,6 +96,7 @@ class LocalPollingMonitorTest extends Specification {
         def handler = Mock(TaskHandler)
         handler.getTask() >> { task }
         handler.canForkProcess() >> true
+        handler.isReady() >> true
 
         expect:
         monitor.canSubmit(handler) == true
@@ -141,6 +142,7 @@ class LocalPollingMonitorTest extends Specification {
         def handler = Mock(TaskHandler)
         handler.getTask() >> { task }
         handler.canForkProcess() >> true
+        handler.isReady() >> true
         
         expect:
         monitor.canSubmit(handler) == true
diff --git a/modules/nextflow/src/test/groovy/nextflow/processor/ParallelPollingMonitorTest.groovy b/modules/nextflow/src/test/groovy/nextflow/processor/ParallelPollingMonitorTest.groovy
index 5fc43aee69..76701ec5e6 100644
--- a/modules/nextflow/src/test/groovy/nextflow/processor/ParallelPollingMonitorTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/processor/ParallelPollingMonitorTest.groovy
@@ -104,6 +104,7 @@ class ParallelPollingMonitorTest extends Specification {
         def result = mon.canSubmit(handler)
         then:
         handler.canForkProcess() >> FORK
+        handler.isReady() >> true
         and:
         result == EXPECTED
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/processor/TaskBeanTest.groovy b/modules/nextflow/src/test/groovy/nextflow/processor/TaskBeanTest.groovy
index c576bef6bb..4cfcb2a1fd 100644
--- a/modules/nextflow/src/test/groovy/nextflow/processor/TaskBeanTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/processor/TaskBeanTest.groovy
@@ -19,6 +19,7 @@ package nextflow.processor
 import java.nio.file.Paths
 
 import nextflow.Session
+import nextflow.conda.CondaConfig
 import nextflow.container.ContainerConfig
 import nextflow.executor.Executor
 import nextflow.script.ProcessConfig
@@ -69,6 +70,7 @@ class TaskBeanTest extends Specification {
         task.getEnvironment() >> [alpha: 'one', beta: 'xxx', gamma: 'yyy']
         task.getContainer() >> 'busybox:latest'
         task.getContainerConfig() >> [docker: true, registry: 'x']
+        task.getCondaConfig() >> new CondaConfig([useMicromamba:true], [:])
 
         when:
         def bean = new TaskBean(task)
@@ -99,6 +101,8 @@ class TaskBeanTest extends Specification {
         bean.stageInMode == 'link'
         bean.stageOutMode == 'rsync'
 
+        bean.useMicromamba == true
+
     }
 
     def 'should clone task bean' () {
diff --git a/modules/nextflow/src/test/groovy/nextflow/processor/TaskConfigTest.groovy b/modules/nextflow/src/test/groovy/nextflow/processor/TaskConfigTest.groovy
index a51d0fc15c..e2a09b1fdf 100644
--- a/modules/nextflow/src/test/groovy/nextflow/processor/TaskConfigTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/processor/TaskConfigTest.groovy
@@ -157,8 +157,8 @@ class TaskConfigTest extends Specification {
 
         where:
         value   | expected
-        null    | 0
-        0       | 0
+        null    | 1
+        0       | 1
         1       | 1
         '3'     | 3
         10      | 10
@@ -171,8 +171,8 @@ class TaskConfigTest extends Specification {
         when:
         config = new TaskConfig()
         then:
-        config.maxRetries == 0
-        config.getMaxRetries() == 0
+        config.maxRetries == 1
+        config.getMaxRetries() == 1
         config.getErrorStrategy() == ErrorStrategy.TERMINATE
 
         when:
diff --git a/modules/nextflow/src/test/groovy/nextflow/processor/TaskHandlerTest.groovy b/modules/nextflow/src/test/groovy/nextflow/processor/TaskHandlerTest.groovy
index df6b065bc9..5bea39a948 100644
--- a/modules/nextflow/src/test/groovy/nextflow/processor/TaskHandlerTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/processor/TaskHandlerTest.groovy
@@ -249,4 +249,18 @@ class TaskHandlerTest extends Specification {
         TaskStatus.RUNNING  | false       | false            | true           | true            | false
         TaskStatus.COMPLETED| false       | false            | false          | false           | true
     }
+
+    @Unroll
+    def 'should include the tower prefix'() {
+        given:
+        def name = 'job_1'
+
+        expect:
+        TaskHandler.prependWorkflowPrefix(name, ENV) == EXPECTED
+
+        where:
+        ENV                         | EXPECTED
+        [:]                         | "job_1"
+        [TOWER_WORKFLOW_ID: '1234'] | "tw-1234-job_1"
+    }
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/processor/TaskRunTest.groovy b/modules/nextflow/src/test/groovy/nextflow/processor/TaskRunTest.groovy
index 9f0cd50875..6f1e988899 100644
--- a/modules/nextflow/src/test/groovy/nextflow/processor/TaskRunTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/processor/TaskRunTest.groovy
@@ -402,7 +402,6 @@ class TaskRunTest extends Specification {
     }
 
     def 'should resolve the task body script' () {
-
         given:
         def task = new TaskRun()
         task.processor = [:] as TaskProcessor
@@ -412,7 +411,7 @@ class TaskRunTest extends Specification {
          * plain task script
          */
         when:
-        task.resolve(new BodyDef({-> 'Hello'}, 'Hello', 'script'))
+        task.resolveBody(new BodyDef({-> 'Hello'}, 'Hello', 'script'))
         then:
         task.script == 'Hello'
         task.source == 'Hello'
@@ -422,7 +421,7 @@ class TaskRunTest extends Specification {
          */
         when:
         task.context = new TaskContext(Mock(Script),[x: 'world'],'foo')
-        task.resolve(new BodyDef({-> "Hello ${x}"}, 'Hello ${x}', 'script'))
+        task.resolveBody(new BodyDef({-> "Hello ${x}"}, 'Hello ${x}', 'script'))
         then:
         task.script == 'Hello world'
         task.source == 'Hello ${x}'
@@ -448,7 +447,7 @@ class TaskRunTest extends Specification {
          */
         when:
         task.context = new TaskContext(Mock(Script),VARS,'foo')
-        task.resolve(new BodyDef(body, 'cat ${one}\nhead ${many}', 'script'))
+        task.resolveBody(new BodyDef(body, 'cat ${one}\nhead ${many}', 'script'))
         then:
         task.script == '''
                     cat a\\ b.txt
@@ -481,7 +480,7 @@ class TaskRunTest extends Specification {
         when:
         task.context = new TaskContext(script,local,'foo')
         task.config = new TaskConfig().setContext(task.context)
-        task.resolve(new BodyDef({-> '$BASH_VAR !{nxf_var} - !{params.var_no}'}, '<the source script>', 'shell'))  // <-- note: 'shell' type
+        task.resolveBody(new BodyDef({-> '$BASH_VAR !{nxf_var} - !{params.var_no}'}, '<the source script>', 'shell'))  // <-- note: 'shell' type
         then:
         task.script == '$BASH_VAR YES - NO'
         task.source == '<the source script>'
@@ -493,7 +492,7 @@ class TaskRunTest extends Specification {
         task.context = new TaskContext(Mock(Script),[nxf_var: '>interpolated value<'],'foo')
         task.config = new TaskConfig().setContext(task.context)
         task.config.placeholder = '#' as char
-        task.resolve(new BodyDef({-> '$BASH_VAR #{nxf_var}'}, '$BASH_VAR #{nxf_var}', 'shell'))  // <-- note: 'shell' type
+        task.resolveBody(new BodyDef({-> '$BASH_VAR #{nxf_var}'}, '$BASH_VAR #{nxf_var}', 'shell'))  // <-- note: 'shell' type
         then:
         task.script == '$BASH_VAR >interpolated value<'
         task.source == '$BASH_VAR #{nxf_var}'
@@ -517,7 +516,7 @@ class TaskRunTest extends Specification {
         task.config = new TaskConfig().setContext(task.context)
 
         when:
-        task.resolve( new BodyDef({-> template(my_file)}, 'template($file)', 'script'))
+        task.resolveBody( new BodyDef({-> template(my_file)}, 'template($file)', 'script'))
         then:
         task.script == 'echo Ciao mondo'
         task.source == 'echo ${say_hello}'
@@ -542,7 +541,7 @@ class TaskRunTest extends Specification {
         task.config = new TaskConfig().setContext(task.context)
 
         when:
-        task.resolve( new BodyDef({-> template(my_file)}, 'template($file)', 'shell'))
+        task.resolveBody( new BodyDef({-> template(my_file)}, 'template($file)', 'shell'))
         then:
         task.script == 'echo $HOME ~ Foo bar'
         task.source == 'echo $HOME ~ !{user_name}'
@@ -568,7 +567,7 @@ class TaskRunTest extends Specification {
         task.config.placeholder = '#' as char
 
         when:
-        task.resolve( new BodyDef({-> template(my_file)}, 'template($file)', 'shell'))
+        task.resolveBody( new BodyDef({-> template(my_file)}, 'template($file)', 'shell'))
         then:
         task.script == 'echo $HOME ~ Foo bar'
         task.source == 'echo $HOME ~ #{user_name}'
@@ -750,7 +749,7 @@ class TaskRunTest extends Specification {
         task.context = GroovyMock(TaskContext)
 
         when:
-        task.resolve(new BodyDef({-> "Hello ${x}"}, 'Hello ${x}', 'script'))
+        task.resolveBody(new BodyDef({-> "Hello ${x}"}, 'Hello ${x}', 'script'))
         and:
         def vars = task.getVariableNames()
         then:
@@ -769,7 +768,7 @@ class TaskRunTest extends Specification {
         task.config = new TaskConfig()
 
         when:
-        task.resolve(new BodyDef({-> 'Hello !{foo} !{bar} !{input_x}'}, 'Hello..', 'shell'))
+        task.resolveBody(new BodyDef({-> 'Hello !{foo} !{bar} !{input_x}'}, 'Hello..', 'shell'))
         and:
         def vars = task.getVariableNames()
         then:
@@ -793,7 +792,7 @@ class TaskRunTest extends Specification {
         task.config = new TaskConfig()
 
         when:
-        task.resolve(new BodyDef({-> template }, 'Hello..', 'script'))
+        task.resolveBody(new BodyDef({-> template }, 'Hello..', 'script'))
         and:
         def vars = task.getVariableNames()
         then:
@@ -822,7 +821,7 @@ class TaskRunTest extends Specification {
          * plain task script
          */
         when:
-        task.resolve(dryRun)
+        task.resolveStub(dryRun)
         then:
         task.script == 'echo Hello world'
         task.source == 'command source'
@@ -891,4 +890,55 @@ class TaskRunTest extends Specification {
         expect:
         !task.isArray()
     }
+
+    def 'should resolve task body' () {
+        given:
+        def task = Spy(TaskRun)
+        task.processor = Mock(TaskProcessor) {
+            getSession()>>Mock(Session) { getStubRun() >> false}
+        }
+        and:
+        def body = Mock(BodyDef)
+
+        when:
+        task.resolve(body)
+        then:
+        1 * task.resolveBody(body) >> null
+        0 * task.resolveStub(_) >> null
+    }
+
+    def 'should resolve task body when no stub' () {
+        given:
+        def task = Spy(TaskRun)
+        task.processor = Mock(TaskProcessor) {
+            getSession()>>Mock(Session) { getStubRun() >> true}
+        }
+        task.config = Mock(TaskConfig) { getStubBlock()>> null }
+        and:
+        def body = Mock(BodyDef)
+
+        when:
+        task.resolve(body)
+        then:
+        1 * task.resolveBody(body) >> null
+        0 * task.resolveStub(_) >> null
+    }
+
+    def 'should resolve task stub' () {
+        given:
+        def body = Mock(BodyDef)
+        def stub = Mock(TaskClosure)
+        and:
+        def task = Spy(TaskRun)
+        task.config = Mock(TaskConfig) { getStubBlock()>>stub }
+        task.processor = Mock(TaskProcessor) {
+            getSession()>>Mock(Session) { getStubRun() >> true}
+        }
+
+        when:
+        task.resolve(body)
+        then:
+        1 * task.resolveStub(stub) >> null
+        0 * task.resolveBody(_) >> null
+    }
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/scm/AssetManagerTest.groovy b/modules/nextflow/src/test/groovy/nextflow/scm/AssetManagerTest.groovy
index aa8bf1467c..ac59065c25 100644
--- a/modules/nextflow/src/test/groovy/nextflow/scm/AssetManagerTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/scm/AssetManagerTest.groovy
@@ -414,7 +414,7 @@ class AssetManagerTest extends Specification {
         then:
         holder.getMainScriptName() == 'main.nf'
         holder.getHomePage() == 'https://github.com/foo/bar'
-        holder.manifest.getDefaultBranch() == 'master'
+        holder.manifest.getDefaultBranch() == null
         holder.manifest.getDescription() == null
 
     }
@@ -601,4 +601,54 @@ class AssetManagerTest extends Specification {
         noExceptionThrown()
     }
 
+    @Requires({System.getenv('NXF_GITHUB_ACCESS_TOKEN')})
+    def 'should identify default branch when downloading repo'() {
+
+        given:
+        def folder = tempDir.getRoot()
+        def token = System.getenv('NXF_GITHUB_ACCESS_TOKEN')
+        def manager = new AssetManager().build('nextflow-io/socks', [providers: [github: [auth: token]]])
+
+        when:
+        // simulate calling `nextflow run nextflow-io/socks` without specifying a revision
+        manager.download()
+        manager.checkout(null)
+        then:
+        folder.resolve('nextflow-io/socks/.git').isDirectory()
+        manager.getCurrentRevision() == 'main'
+
+        when:
+        manager.download()
+        then:
+        noExceptionThrown()
+    }
+
+    @Requires({System.getenv('NXF_GITHUB_ACCESS_TOKEN')})
+    def 'can filter remote branches'() {
+        given:
+        def folder = tempDir.getRoot()
+        def token = System.getenv('NXF_GITHUB_ACCESS_TOKEN')
+        def manager = new AssetManager().build('nextflow-io/hello', [providers: [github: [auth: token]]])
+        manager.download()
+        def branches = manager.getBranchList()
+
+        when:
+        def remote_head = branches.find { it.name == 'refs/remotes/origin/HEAD' }
+        then:
+        remote_head != null
+        !AssetManager.isRemoteBranch(remote_head)
+
+        when:
+        def remote_master = branches.find { it.name == 'refs/remotes/origin/master' }
+        then:
+        remote_master != null
+        AssetManager.isRemoteBranch(remote_master)
+
+        when:
+        def local_master = branches.find { it.name == 'refs/heads/master' }
+        then:
+        local_master != null
+        !AssetManager.isRemoteBranch(local_master)
+    }
+
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/scm/AzureRepositoryProviderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/scm/AzureRepositoryProviderTest.groovy
index 00e7cc74f0..decec42c1d 100644
--- a/modules/nextflow/src/test/groovy/nextflow/scm/AzureRepositoryProviderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/scm/AzureRepositoryProviderTest.groovy
@@ -80,7 +80,7 @@ class AzureRepositoryProviderTest extends Specification {
         def obj = new ProviderConfig('azurerepos', config.providers.azurerepos as ConfigObject)
 
         expect:
-        new AzureRepositoryProvider('ORGANIZATION/PROJECT/hello', obj).getRepositoryUrl() == 'https://dev.azure.com/ORGANIZATION/PROJECT'
+        new AzureRepositoryProvider('ORGANIZATION/PROJECT/hello', obj).getRepositoryUrl() == 'https://dev.azure.com/ORGANIZATION/PROJECT/hello'
 
     }
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/OutputDslTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/OutputDslTest.groovy
index 3828ae5fc4..265672fd3f 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/OutputDslTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/OutputDslTest.groovy
@@ -18,15 +18,23 @@ class OutputDslTest extends Specification {
     def 'should publish workflow outputs'() {
         given:
         def root = Files.createTempDirectory('test')
+        def outputDir = root.resolve('results')
         def workDir = root.resolve('work')
         def work1 = workDir.resolve('ab/1234'); Files.createDirectories(work1)
         def work2 = workDir.resolve('cd/5678'); Files.createDirectories(work2)
         def file1 = work1.resolve('file1.txt'); file1.text = 'Hello'
         def file2 = work2.resolve('file2.txt'); file2.text = 'world'
-        def target = root.resolve('results')
         and:
         def session = Mock(Session) {
-            getConfig() >> [:]
+            getConfig() >> [
+                workflow: [
+                    output: [
+                        mode: 'symlink',
+                        overwrite: true
+                    ]
+                ]
+            ]
+            getOutputDir() >> outputDir
             getWorkDir() >> workDir
         }
         Global.session = session
@@ -48,9 +56,6 @@ class OutputDslTest extends Specification {
         SysEnv.push(NXF_FILE_ROOT: root.toString())
 
         when:
-        dsl.directory('results')
-        dsl.mode('symlink')
-        dsl.overwrite(true)
         dsl.target('bar') {
             path('barbar')
             index {
@@ -67,74 +72,69 @@ class OutputDslTest extends Specification {
         }
 
         then:
-        target.resolve('foo/file1.txt').text == 'Hello'
-        target.resolve('barbar/file2.txt').text == 'world'
-        target.resolve('barbar/index.csv').text == """\
-            "file2","${target}/barbar/file2.txt"
+        outputDir.resolve('foo/file1.txt').text == 'Hello'
+        outputDir.resolve('barbar/file2.txt').text == 'world'
+        outputDir.resolve('barbar/index.csv').text == """\
+            "file2","${outputDir}/barbar/file2.txt"
             """.stripIndent()
         and:
-        1 * session.notifyFilePublish(target.resolve('foo/file1.txt'), file1)
-        1 * session.notifyFilePublish(target.resolve('barbar/file2.txt'), file2)
-        1 * session.notifyFilePublish(target.resolve('barbar/index.csv'))
+        1 * session.notifyFilePublish(outputDir.resolve('foo/file1.txt'), file1)
+        1 * session.notifyFilePublish(outputDir.resolve('barbar/file2.txt'), file2)
+        1 * session.notifyFilePublish(outputDir.resolve('barbar/index.csv'))
 
         cleanup:
         SysEnv.pop()
         root?.deleteDir()
     }
 
-    def 'should set options' () {
+    def 'should set target dsl' () {
         when:
-        def dsl1 = new OutputDsl()
+        def dsl1 = new OutputDsl.TargetDsl()
         then:
-        dsl1.@defaults == [:]
+        dsl1.getOptions() == [:]
 
         when:
-        def dsl2 = new OutputDsl()
+        def dsl2 = new OutputDsl.TargetDsl()
         and:
         dsl2.contentType('simple/text')
+        dsl2.enabled(true)
         dsl2.ignoreErrors(true)
         dsl2.mode('someMode')
         dsl2.overwrite(true)
         dsl2.storageClass('someClass')
         dsl2.tags([foo:'1',bar:'2'])
-        dsl2.enabled(true)
         then:
-        dsl2.@defaults == [
+        dsl2.getOptions() == [
             contentType:'simple/text',
+            enabled: true,
             ignoreErrors: true,
             mode: 'someMode',
             overwrite: true,
             storageClass: 'someClass',
-            tags: [foo:'1',bar:'2'],
-            enabled: true
+            tags: [foo:'1',bar:'2']
         ]
     }
 
-    def 'should set target dsl' () {
+    def 'should set index dsl' () {
         when:
-        def dsl1 = new OutputDsl.TargetDsl()
+        def dsl1 = new OutputDsl.IndexDsl()
         then:
         dsl1.getOptions() == [:]
 
         when:
-        def dsl2 = new OutputDsl.TargetDsl()
+        def dsl2 = new OutputDsl.IndexDsl()
+        def mapper = { v -> v }
         and:
-        dsl2.contentType('simple/text')
-        dsl2.ignoreErrors(true)
-        dsl2.mode('someMode')
-        dsl2.overwrite(true)
-        dsl2.storageClass('someClass')
-        dsl2.tags([foo:'1',bar:'2'])
-        dsl2.enabled(true)
+        dsl2.header(true)
+        dsl2.mapper(mapper)
+        dsl2.path('path')
+        dsl2.sep(',')
         then:
         dsl2.getOptions() == [
-            contentType:'simple/text',
-            ignoreErrors: true,
-            mode: 'someMode',
-            overwrite: true,
-            storageClass: 'someClass',
-            tags: [foo:'1',bar:'2'],
-            enabled: true
+            header: true,
+            mapper: mapper,
+            path: 'path',
+            sep: ','
         ]
     }
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/ProcessConfigTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/ProcessConfigTest.groovy
index bad0784768..59dd323c7f 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/ProcessConfigTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/ProcessConfigTest.groovy
@@ -47,7 +47,7 @@ class ProcessConfigTest extends Specification {
         expect:
         config.shell ==  ['/bin/bash','-ue']
         config.cacheable
-        config.maxRetries == 0
+        config.maxRetries == 1
         config.maxErrors == -1
         config.errorStrategy == ErrorStrategy.TERMINATE
     }
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/ScriptBindingTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/ScriptBindingTest.groovy
index e65f0c10ac..59ca5c6ecc 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/ScriptBindingTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/ScriptBindingTest.groovy
@@ -75,65 +75,30 @@ class ScriptBindingTest extends Specification {
 
     }
 
-    def 'should convert hyphen separated string to camel case' () {
-
-        expect:
-        ScriptBinding.ParamsMap.hyphenToCamelCase('a') == 'a'
-        ScriptBinding.ParamsMap.hyphenToCamelCase('A') == 'A'
-        ScriptBinding.ParamsMap.hyphenToCamelCase('a-b-c-') == 'aBC'
-        ScriptBinding.ParamsMap.hyphenToCamelCase('aa-bb-cc') == 'aaBbCc'
-        ScriptBinding.ParamsMap.hyphenToCamelCase('alpha-beta-delta') == 'alphaBetaDelta'
-        ScriptBinding.ParamsMap.hyphenToCamelCase('Alpha-Beta-delta') == 'AlphaBetaDelta'
-
-    }
-
-    def 'should convert camel case string to hyphen separated' () {
-
-        expect:
-        ScriptBinding.ParamsMap.camelCaseToHyphen('alphaBetaDelta') == 'alpha-beta-delta'
-        ScriptBinding.ParamsMap.camelCaseToHyphen('AlphaBetaDelta') == 'Alpha-beta-delta'
-        ScriptBinding.ParamsMap.camelCaseToHyphen('Field1') == 'Field1'
-        ScriptBinding.ParamsMap.camelCaseToHyphen('FieldUno') == 'Field-uno'
-        ScriptBinding.ParamsMap.camelCaseToHyphen('FieldUNO') == 'Field-UNO'
-        ScriptBinding.ParamsMap.camelCaseToHyphen('FieldA') == 'Field-A'
-        ScriptBinding.ParamsMap.camelCaseToHyphen('FieldAB') == 'Field-AB'
-        ScriptBinding.ParamsMap.camelCaseToHyphen('FieldAb') == 'Field-ab'
-
-    }
-
     def 'should put an entry in the params map' () {
 
         when:
         def map = new ScriptBinding.ParamsMap()
         map['alphaBeta'] = 1
         map['alphaBeta'] = 2
-        map['alpha-beta'] = 3
-
         then:
         map['alphaBeta'] == 1
-        map['alpha-beta'] == 1
-
 
         when:
         map = new ScriptBinding.ParamsMap()
-        map['aaa-bbb-ccc'] = 1
         map['aaaBbbCcc'] = 10
         map['AaaBbbCcc'] = 20
-
         then:
-        map['aaaBbbCcc'] == 1
-        map['aaa-bbb-ccc'] == 1
-
+        map['aaaBbbCcc'] == 10
+        map['AaaBbbCcc'] == 20
 
         when:
         map = new ScriptBinding.ParamsMap()
         map['field1'] = 1
         map['field2'] = 2
         map['Field2'] = 3
-
         then:
         map['field1'] == 1
-        map['field-1'] == null
         map['field2']  == 2
         map['Field2']  == 3
 
@@ -151,7 +116,6 @@ class ScriptBindingTest extends Specification {
         then:
         map.alpha == 0
         map.alphaBeta == 0
-        map.'alpha-beta' == 0
         map.delta == 2
         map.gamma == 3
 
@@ -160,7 +124,6 @@ class ScriptBindingTest extends Specification {
         then:
         copy.foo == 1
         copy.alphaBeta == 4
-        copy.'alpha-beta' == 4
         copy.delta == 2
         copy.gamma == 3
         copy.omega == 9
@@ -168,46 +131,12 @@ class ScriptBindingTest extends Specification {
         // source does not change
         map.alpha == 0
         map.alphaBeta == 0
-        map.'alpha-beta' == 0
         map.delta == 2
         map.gamma == 3
         !map.containsKey('omega')
 
     }
 
-    def 'should wrap a string value with quote character' () {
-
-        expect:
-        ScriptBinding.ParamsMap.wrap('hello',null) == 'hello'
-        ScriptBinding.ParamsMap.wrap('hello','"') == '"hello"'
-        ScriptBinding.ParamsMap.wrap('hello world',null) == '"hello world"'
-        ScriptBinding.ParamsMap.wrap('hello world',"'") == "'hello world'"
-        ScriptBinding.ParamsMap.wrap('hello"world',"'") == "'hello\"world'"
-        ScriptBinding.ParamsMap.wrap('hello"world',null) == '"hello\\"world"'
-
-    }
-
-    def 'should return a command line formatted string'() {
-
-        when:
-        def params = new ScriptBinding.ParamsMap('foo-bar':1)
-        then:
-        params.size() == 2
-        params.fooBar == 1
-        params.'foo-bar' == 1
-        params.all() == '--foo-bar 1'
-
-        expect:
-        new ScriptBinding.ParamsMap(x:1).all() == '--x 1'
-        new ScriptBinding.ParamsMap(x:1, y: 2).all() == '--x 1 --y 2'
-        new ScriptBinding.ParamsMap(x:1, y: 2).all(sep:'=') == '--x=1 --y=2'
-        new ScriptBinding.ParamsMap(x:1, y: 2).all(sep:'=', prefix:'-') == '-x=1 -y=2'
-        new ScriptBinding.ParamsMap(x:1, y: 'hello world').all() == '--x 1 --y "hello world"'
-        new ScriptBinding.ParamsMap(x:1, y: 'hello world').all(quote:"'") == '--x \'1\' --y \'hello world\''
-        new ScriptBinding.ParamsMap(x:1, y: "O'Connors").all(quote:"'") == "--x '1' --y 'O\\'Connors'"
-
-    }
-
     def 'should get the variable name giving the value'() {
 
         given:
diff --git a/modules/nextflow/src/test/groovy/nextflow/trace/ProgressRecordTest.groovy b/modules/nextflow/src/test/groovy/nextflow/trace/ProgressRecordTest.groovy
index e9541d2dda..e8fecc07b5 100644
--- a/modules/nextflow/src/test/groovy/nextflow/trace/ProgressRecordTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/trace/ProgressRecordTest.groovy
@@ -60,6 +60,7 @@ class ProgressRecordTest extends Specification {
         def FAILED =5
         def CACHED =6
         def STORED =7
+        def ABORTED = 8
         and:
         def rec = new ProgressRecord(10, 'foo')
 
@@ -71,10 +72,11 @@ class ProgressRecordTest extends Specification {
         rec.failed =FAILED
         rec.cached =CACHED
         rec.stored =STORED
+        rec.aborted = ABORTED
 
         then:
         rec.getCompletedCount() == SUCCEEDED+ FAILED+ CACHED+ STORED
-        rec.getTotalCount() == PENDING+ SUBMITTED+ RUNNING + SUCCEEDED+ FAILED+ CACHED+ STORED
+        rec.getTotalCount() == PENDING+ SUBMITTED+ RUNNING + SUCCEEDED+ FAILED+ CACHED+ STORED+ ABORTED
     }
 
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/util/ArrayBagTest.groovy b/modules/nextflow/src/test/groovy/nextflow/util/ArrayBagTest.groovy
index 0eb91521a6..b4e0b8efb4 100644
--- a/modules/nextflow/src/test/groovy/nextflow/util/ArrayBagTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/util/ArrayBagTest.groovy
@@ -74,4 +74,35 @@ class ArrayBagTest extends Specification {
         String.valueOf(bag) == '[1, 2, 3]'
     }
 
+    def 'hashCode should be invariant to order' () {
+        given:
+        def bag1 = new ArrayBag([1,2,3])
+        def bag2 = new ArrayBag([3,1,2])
+        def bag3 = new ArrayBag([4,1,2])
+
+        expect:
+        bag1.hashCode() == bag2.hashCode()
+        bag1.hashCode() != bag3.hashCode()
+
+        /**
+         * NOTE!!! equality cannot be checked due to groovy overriding the equals implementation
+         * see {@link ArrayBag#equals(java.lang.Object)}
+         */
+    }
+
+    def 'should access map entry using bag as key' () {
+        given:
+        def bag1 = new ArrayBag([1,2,3])
+        def bag2 = new ArrayBag([3,1,2])
+        def bag3 = new ArrayBag([4,1,2])
+        and:
+        def map = [(bag1):'foo']
+
+        expect:
+        map.get(bag1) == 'foo'
+        map.get(bag2) == 'foo'
+        map.get(bag3) == null
+
+    }
+
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/util/ConfigHelperTest.groovy b/modules/nextflow/src/test/groovy/nextflow/util/ConfigHelperTest.groovy
index b92ec8c308..985038ca1f 100644
--- a/modules/nextflow/src/test/groovy/nextflow/util/ConfigHelperTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/util/ConfigHelperTest.groovy
@@ -19,6 +19,7 @@ package nextflow.util
 import java.nio.file.Files
 import java.nio.file.Paths
 
+import nextflow.config.ConfigClosurePlaceholder
 import spock.lang.Specification
 import spock.lang.Unroll
 
@@ -245,6 +246,100 @@ class ConfigHelperTest extends Specification {
 
     }
 
+    def 'should render config as json' () {
+        given:
+        def config = new ConfigObject()
+        config.process.queue = 'long'
+        config.process.executor = 'slurm'
+        config.process.memory = new ConfigClosurePlaceholder('{ 1.GB }')
+        config.docker.enabled = true
+        config.zeta.'quoted-attribute'.foo = 1
+
+        when:
+        def result = ConfigHelper.toJsonString(config, true)
+        then:
+        result == '''
+            {
+                "docker": {
+                    "enabled": true
+                },
+                "process": {
+                    "executor": "slurm",
+                    "memory": "{ 1.GB }",
+                    "queue": "long"
+                },
+                "zeta": {
+                    "quoted-attribute": {
+                        "foo": 1
+                    }
+                }
+            }
+            '''.stripIndent().trim()
+
+
+        when:
+        result = ConfigHelper.toJsonString(config, false)
+        then:
+        result == '''
+            {
+                "process": {
+                    "queue": "long",
+                    "executor": "slurm",
+                    "memory": "{ 1.GB }"
+                },
+                "docker": {
+                    "enabled": true
+                },
+                "zeta": {
+                    "quoted-attribute": {
+                        "foo": 1
+                    }
+                }
+            }
+            '''.stripIndent().trim()
+    }
+
+    def 'should render config as yaml' () {
+        given:
+        def config = new ConfigObject()
+        config.process.queue = 'long'
+        config.process.executor = 'slurm'
+        config.process.memory = new ConfigClosurePlaceholder('{ 1.GB }')
+        config.docker.enabled = true
+        config.zeta.'quoted-attribute'.foo = 1
+
+        when:
+        def result = ConfigHelper.toYamlString(config, true)
+        then:
+        result == '''\
+            docker:
+              enabled: true
+            process:
+              executor: slurm
+              memory: '{ 1.GB }'
+              queue: long
+            zeta:
+              quoted-attribute:
+                foo: 1
+            '''.stripIndent()
+
+
+        when:
+        result = ConfigHelper.toYamlString(config, false)
+        then:
+        result == '''\
+            process:
+              queue: long
+              executor: slurm
+              memory: '{ 1.GB }'
+            docker:
+              enabled: true
+            zeta:
+              quoted-attribute:
+                foo: 1
+            '''.stripIndent()
+    }
+
     def 'should verify valid identifiers' () {
 
         expect:
diff --git a/modules/nextflow/src/test/groovy/nextflow/util/KryoHelperTest.groovy b/modules/nextflow/src/test/groovy/nextflow/util/KryoHelperTest.groovy
index eea8009514..35c3ef6352 100644
--- a/modules/nextflow/src/test/groovy/nextflow/util/KryoHelperTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/util/KryoHelperTest.groovy
@@ -165,6 +165,16 @@ class KryoHelperTest extends  Specification {
         KryoHelper.deserialize(buffer).toUri() == new URI('http://host.com/foo.txt')
     }
 
+    def 'should serialise xfilesystem' () {
+        when:
+        def uri = new URI('https://host.com/path/foo.txt')
+        def fs = FileHelper.getOrCreateFileSystemFor(new URI('https://host.com/path/foo.txt'))
+        def fsBuffer = KryoHelper.serialize(fs)
+        then:
+        KryoHelper.deserialize(fsBuffer).getClass().getName() == 'nextflow.file.http.XFileSystem'
+        KryoHelper.deserialize(fsBuffer).getPath("/path/foo.txt").toUri() == uri
+    }
+
     @EqualsAndHashCode
     static class Foo implements SerializableMarker {
         String foo
diff --git a/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt b/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt
index ef1380e7cf..5aef2f4795 100644
--- a/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt
+++ b/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt
@@ -98,26 +98,28 @@ nxf_mem_watch() {
         count=$((count+1))
     done
 
-    echo "%mem=${nxf_stat_ret[1]}"      >> $trace_file
-    echo "vmem=${nxf_stat_ret[2]}"      >> $trace_file
-    echo "rss=${nxf_stat_ret[3]}"       >> $trace_file
-    echo "peak_vmem=${nxf_stat_ret[4]}" >> $trace_file
-    echo "peak_rss=${nxf_stat_ret[5]}"  >> $trace_file
-    echo "vol_ctxt=${nxf_stat_ret[6]}"  >> $trace_file
-    echo "inv_ctxt=${nxf_stat_ret[7]}"  >> $trace_file
+    printf "%s\n" \
+        "%mem=${nxf_stat_ret[1]}" \
+        "vmem=${nxf_stat_ret[2]}" \
+        "rss=${nxf_stat_ret[3]}" \
+        "peak_vmem=${nxf_stat_ret[4]}" \
+        "peak_rss=${nxf_stat_ret[5]}" \
+        "vol_ctxt=${nxf_stat_ret[6]}" \
+        "inv_ctxt=${nxf_stat_ret[7]}" >> "$trace_file" || >&2 echo "Error: Failed to append to file: $trace_file"
 }
 
 nxf_write_trace() {
-    echo "nextflow.trace/v2"           > $trace_file
-    echo "realtime=$wall_time"         >> $trace_file
-    echo "%cpu=$ucpu"                  >> $trace_file
-    echo "cpu_model=$cpu_model"        >> $trace_file
-    echo "rchar=${io_stat1[0]}"        >> $trace_file
-    echo "wchar=${io_stat1[1]}"        >> $trace_file
-    echo "syscr=${io_stat1[2]}"        >> $trace_file
-    echo "syscw=${io_stat1[3]}"        >> $trace_file
-    echo "read_bytes=${io_stat1[4]}"   >> $trace_file
-    echo "write_bytes=${io_stat1[5]}"  >> $trace_file
+    printf "%s\n" \
+        "nextflow.trace/v2" \
+        "realtime=$wall_time" \
+        "%cpu=$ucpu" \
+        "cpu_model=$cpu_model" \
+        "rchar=${io_stat1[0]}" \
+        "wchar=${io_stat1[1]}" \
+        "syscr=${io_stat1[2]}" \
+        "syscw=${io_stat1[3]}" \
+        "read_bytes=${io_stat1[4]}" \
+        "write_bytes=${io_stat1[5]}" > "$trace_file" || >&2 echo "Error: Failed to write to file: $trace_file"
 }
 
 nxf_trace_mac() {
@@ -173,16 +175,17 @@ nxf_trace_linux() {
     local wall_time=$((end_millis-start_millis))
     [ $NXF_DEBUG = 1 ] && echo "+++ STATS %CPU=$ucpu TIME=$wall_time I/O=${io_stat1[*]}"
 
-    echo "nextflow.trace/v2"           > $trace_file
-    echo "realtime=$wall_time"         >> $trace_file
-    echo "%cpu=$ucpu"                  >> $trace_file
-    echo "cpu_model=$cpu_model"        >> $trace_file
-    echo "rchar=${io_stat1[0]}"        >> $trace_file
-    echo "wchar=${io_stat1[1]}"        >> $trace_file
-    echo "syscr=${io_stat1[2]}"        >> $trace_file
-    echo "syscw=${io_stat1[3]}"        >> $trace_file
-    echo "read_bytes=${io_stat1[4]}"   >> $trace_file
-    echo "write_bytes=${io_stat1[5]}"  >> $trace_file
+    printf "%s\n" \
+        "nextflow.trace/v2" \
+        "realtime=$wall_time" \
+        "%cpu=$ucpu" \
+        "cpu_model=$cpu_model" \
+        "rchar=${io_stat1[0]}" \
+        "wchar=${io_stat1[1]}" \
+        "syscr=${io_stat1[2]}" \
+        "syscw=${io_stat1[3]}" \
+        "read_bytes=${io_stat1[4]}" \
+        "write_bytes=${io_stat1[5]}" > "$trace_file" || >&2 echo "Error: Failed to write to file: $trace_file"
 
     [ -e /proc/$mem_proc ] && eval "echo 'DONE' >&$mem_fd" || true
     wait $mem_proc 2>/dev/null || true
@@ -270,7 +273,10 @@ nxf_fs_fcp() {
 }
 
 on_exit() {
-    exit_status=${nxf_main_ret:=$?}
+    local last_err=$?
+    local exit_status=${nxf_main_ret:=0}
+    [[ ${exit_status} -eq 0 && ${nxf_unstage_ret:=0} -ne 0 ]] && exit_status=${nxf_unstage_ret:=0}
+    [[ ${exit_status} -eq 0 && ${last_err} -ne 0 ]] && exit_status=${last_err}
     printf -- $exit_status > {{folder}}/.exitcode
     set +u
     exit $exit_status
@@ -289,9 +295,20 @@ nxf_stage() {
     true
 }
 
-nxf_unstage() {
+nxf_unstage_outputs() {
+    true
+}
+
+nxf_unstage_controls() {
     true
-    [[ ${nxf_main_ret:=0} != 0 ]] && return
+}
+
+nxf_unstage() {
+    if [[ ${nxf_main_ret:=0} == 0 ]]; then
+        (set -e -o pipefail; (nxf_unstage_outputs | tee -a .command.out) 3>&1 1>&2 2>&3 | tee -a .command.err)
+        nxf_unstage_ret=$?
+    fi
+    nxf_unstage_controls
 }
 
 nxf_main() {
diff --git a/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper.txt b/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper.txt
index f465b5b9b4..3bb4f34fe5 100644
--- a/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper.txt
+++ b/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper.txt
@@ -81,7 +81,10 @@ nxf_fs_fcp() {
 }
 
 on_exit() {
-    exit_status=${nxf_main_ret:=$?}
+    local last_err=$?
+    local exit_status=${nxf_main_ret:=0}
+    [[ ${exit_status} -eq 0 && ${nxf_unstage_ret:=0} -ne 0 ]] && exit_status=${nxf_unstage_ret:=0}
+    [[ ${exit_status} -eq 0 && ${last_err} -ne 0 ]] && exit_status=${last_err}
     printf -- $exit_status > {{folder}}/.exitcode
     set +u
     exit $exit_status
@@ -100,9 +103,20 @@ nxf_stage() {
     true
 }
 
-nxf_unstage() {
+nxf_unstage_outputs() {
+    true
+}
+
+nxf_unstage_controls() {
     true
-    [[ ${nxf_main_ret:=0} != 0 ]] && return
+}
+
+nxf_unstage() {
+    if [[ ${nxf_main_ret:=0} == 0 ]]; then
+        (set -e -o pipefail; (nxf_unstage_outputs | tee -a .command.out) 3>&1 1>&2 2>&3 | tee -a .command.err)
+        nxf_unstage_ret=$?
+    fi
+    nxf_unstage_controls
 }
 
 nxf_main() {
diff --git a/modules/nextflow/src/testFixtures/groovy/test/MockHelpers.groovy b/modules/nextflow/src/testFixtures/groovy/test/MockHelpers.groovy
index 5a0c0c1c39..51a298dbd6 100644
--- a/modules/nextflow/src/testFixtures/groovy/test/MockHelpers.groovy
+++ b/modules/nextflow/src/testFixtures/groovy/test/MockHelpers.groovy
@@ -175,7 +175,7 @@ class MockTaskHandler extends TaskHandler {
             task.code.call()
         }
         status = TaskStatus.COMPLETED
-        task.processor.finalizeTask(task)
+        task.processor.finalizeTask(this)
     }
 
     @Override
diff --git a/modules/nf-commons/build.gradle b/modules/nf-commons/build.gradle
index 2a5c6ec708..951bf44f23 100644
--- a/modules/nf-commons/build.gradle
+++ b/modules/nf-commons/build.gradle
@@ -26,8 +26,8 @@ sourceSets {
 
 dependencies {
     api "ch.qos.logback:logback-classic:1.4.14"
-    api "org.apache.groovy:groovy:4.0.22"
-    api "org.apache.groovy:groovy-nio:4.0.22"
+    api "org.apache.groovy:groovy:4.0.24"
+    api "org.apache.groovy:groovy-nio:4.0.24"
     api "commons-lang:commons-lang:2.6"
     api 'com.google.guava:guava:33.0.0-jre'
     api 'org.pf4j:pf4j:3.12.0'
diff --git a/modules/nf-commons/src/main/nextflow/file/CopyMoveHelper.java b/modules/nf-commons/src/main/nextflow/file/CopyMoveHelper.java
index 7c978e65d2..e5b3c13d8a 100644
--- a/modules/nf-commons/src/main/nextflow/file/CopyMoveHelper.java
+++ b/modules/nf-commons/src/main/nextflow/file/CopyMoveHelper.java
@@ -41,6 +41,10 @@
  * Helper class to handle copy/move files and directories
  */
 public class CopyMoveHelper {
+    /**
+     * True if currently performing a copy of a foreign file.
+     */
+    public static final ThreadLocal<Boolean> IN_FOREIGN_COPY = new ThreadLocal<>();
 
     private static Logger log = LoggerFactory.getLogger(CopyMoveHelper.class);
 
@@ -81,14 +85,16 @@ private static CopyOption[] convertMoveToCopyOptions(CopyOption... options)
     private static void copyFile(Path source, Path target, boolean foreign, CopyOption... options)
             throws IOException
     {
-
         if( !foreign ) {
             source.getFileSystem().provider().copy(source, target, options);
             return;
         }
 
+        IN_FOREIGN_COPY.set(true);
         try (InputStream in = Files.newInputStream(source)) {
             Files.copy(in, target);
+        } finally {
+            IN_FOREIGN_COPY.set(false);
         }
     }
 
diff --git a/modules/nf-httpfs/build.gradle b/modules/nf-httpfs/build.gradle
index ba7e9462f6..29fc92922c 100644
--- a/modules/nf-httpfs/build.gradle
+++ b/modules/nf-httpfs/build.gradle
@@ -30,12 +30,12 @@ sourceSets {
 dependencies {
     api project(':nf-commons')
     api "ch.qos.logback:logback-classic:1.4.14"
-    api "org.apache.groovy:groovy:4.0.22"
-    api "org.apache.groovy:groovy-nio:4.0.22"
+    api "org.apache.groovy:groovy:4.0.24"
+    api "org.apache.groovy:groovy-nio:4.0.24"
     api("com.esotericsoftware.kryo:kryo:2.24.0") { exclude group: 'com.esotericsoftware.minlog', module: 'minlog' }
 
     /* testImplementation inherited from top gradle build file */
-    testImplementation "org.apache.groovy:groovy-json:4.0.22" // needed by wiremock
+    testImplementation "org.apache.groovy:groovy-json:4.0.24" // needed by wiremock
     testImplementation ('com.github.tomakehurst:wiremock:1.57') { exclude module: 'groovy-all' }
     testImplementation ('com.github.tomjankes:wiremock-groovy:0.2.0') { exclude module: 'groovy-all' }
 
diff --git a/modules/nf-httpfs/src/main/nextflow/file/http/FixedInputStream.groovy b/modules/nf-httpfs/src/main/nextflow/file/http/FixedInputStream.groovy
new file mode 100644
index 0000000000..3f6e100af4
--- /dev/null
+++ b/modules/nf-httpfs/src/main/nextflow/file/http/FixedInputStream.groovy
@@ -0,0 +1,73 @@
+/*
+ * Copyright 2013-2024, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.file.http
+
+import groovy.transform.CompileStatic
+
+/**
+ * Implements a {@link FilterInputStream} that checks the expected length of bytes have been
+ * read when closing the stream or throws an error otherwise
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+@CompileStatic
+class FixedInputStream extends FilterInputStream {
+
+    private final long length
+    private long bytesRead
+
+    FixedInputStream(InputStream inputStream, long len) {
+        super(inputStream)
+        this.length = len
+    }
+
+    @Override
+    int read() throws IOException {
+        final result = super.read()
+        if( result!=-1 )
+            bytesRead++
+        return result
+    }
+
+    @Override
+    int read(byte[] b, int off, int len) throws IOException {
+        final result = super.read(b, off, len)
+        if( result!=-1 )
+            bytesRead += result
+        return result
+    }
+
+    @Override
+    long skip(long n) throws IOException {
+        long skipped = super.skip(n)
+        bytesRead += skipped
+        return skipped
+    }
+
+    @Override
+    int available() throws IOException {
+        super.available()
+    }
+
+    @Override
+    void close() throws IOException {
+        if( bytesRead != length )
+            throw new IOException("Read data length does not match expected size - bytes read: ${bytesRead}; expected: ${length}")
+        super.close()
+    }
+}
diff --git a/modules/nf-httpfs/src/main/nextflow/file/http/XFileSystem.groovy b/modules/nf-httpfs/src/main/nextflow/file/http/XFileSystem.groovy
index d62455dff7..3e47953af7 100644
--- a/modules/nf-httpfs/src/main/nextflow/file/http/XFileSystem.groovy
+++ b/modules/nf-httpfs/src/main/nextflow/file/http/XFileSystem.groovy
@@ -44,6 +44,11 @@ class XFileSystem extends FileSystem {
 
     private URI base
 
+    /*
+    * Only needed to prevent serialization issues - see https://github.com/nextflow-io/nextflow/issues/5208
+    */
+    protected XFileSystem(){}
+
     XFileSystem(XFileSystemProvider provider, URI base) {
         this.provider = provider
         this.base = base
diff --git a/modules/nf-httpfs/src/main/nextflow/file/http/XFileSystemProvider.groovy b/modules/nf-httpfs/src/main/nextflow/file/http/XFileSystemProvider.groovy
index e673a930c1..8bfdaae560 100644
--- a/modules/nf-httpfs/src/main/nextflow/file/http/XFileSystemProvider.groovy
+++ b/modules/nf-httpfs/src/main/nextflow/file/http/XFileSystemProvider.groovy
@@ -16,6 +16,8 @@
 
 package nextflow.file.http
 
+import nextflow.file.CopyMoveHelper
+
 import static nextflow.file.http.XFileSystemConfig.*
 
 import java.nio.ByteBuffer
@@ -245,7 +247,11 @@ abstract class XFileSystemProvider extends FileSystemProvider {
         }
 
         final conn = toConnection(path)
-        final stream = new BufferedInputStream(conn.getInputStream())
+        final length = conn.getContentLengthLong()
+        final target = length>0
+                ? new FixedInputStream(conn.getInputStream(),length)
+                : conn.getInputStream()
+        final stream = new BufferedInputStream(target)
 
         new SeekableByteChannel() {
 
@@ -346,7 +352,12 @@ abstract class XFileSystemProvider extends FileSystemProvider {
             }
         }
 
-        return toConnection(path).getInputStream()
+        final conn = toConnection(path)
+        final length = conn.getContentLengthLong()
+        // only apply the FixedInputStream check if staging files
+        return length>0 && CopyMoveHelper.IN_FOREIGN_COPY.get()
+            ? new FixedInputStream(conn.getInputStream(), length)
+            : conn.getInputStream()
     }
 
     /**
diff --git a/modules/nf-httpfs/src/main/nextflow/file/http/XPath.groovy b/modules/nf-httpfs/src/main/nextflow/file/http/XPath.groovy
index 4a3ddb5164..d2c7401734 100644
--- a/modules/nf-httpfs/src/main/nextflow/file/http/XPath.groovy
+++ b/modules/nf-httpfs/src/main/nextflow/file/http/XPath.groovy
@@ -45,6 +45,11 @@ class XPath implements Path {
 
     private String query
 
+    /*
+     * Only needed to prevent serialization issues - see https://github.com/nextflow-io/nextflow/issues/5208
+     */
+    protected XPath(){}
+
     XPath(XFileSystem fs, String path) {
         this(fs, path, EMPTY)
     }
diff --git a/modules/nf-httpfs/src/test/nextflow/file/http/FixedInputStreamTest.groovy b/modules/nf-httpfs/src/test/nextflow/file/http/FixedInputStreamTest.groovy
new file mode 100644
index 0000000000..96ae2134b1
--- /dev/null
+++ b/modules/nf-httpfs/src/test/nextflow/file/http/FixedInputStreamTest.groovy
@@ -0,0 +1,79 @@
+/*
+ * Copyright 2013-2024, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.file.http
+
+import spock.lang.Specification
+
+/**
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+class FixedInputStreamTest extends Specification {
+
+    def 'should read byte by byte' () {
+        given:
+        def bytes = "Hello world". bytes
+        def stream = new FixedInputStream(new ByteArrayInputStream(bytes), bytes.length)
+
+        when:
+        def ch
+        def result = new StringBuilder()
+        while( (ch=stream.read())!=-1 )
+            result.append(ch as char)
+        and:
+        stream.close()
+        then:
+        noExceptionThrown()
+        result.toString() == 'Hello world'
+    }
+
+    def 'should read byte buffer' () {
+        given:
+        def bytes = "Hello world". bytes
+        def stream = new FixedInputStream(new ByteArrayInputStream(bytes), bytes.length)
+
+        when:
+        def buffer = new byte[5]
+        def result = new StringBuilder()
+        def c
+        while( (c=stream.read(buffer))!=-1 ) {
+            for( int i=0; i<c; i++ )
+                result.append(buffer[i] as char)
+        }
+        and:
+        stream.close()
+        then:
+        noExceptionThrown()
+        result.toString() == 'Hello world'
+    }
+
+    def 'should read all bytes' () {
+        given:
+        def bytes = "Hello world". bytes
+        def stream = new FixedInputStream(new ByteArrayInputStream(bytes), bytes.length)
+
+        when:
+        def result = stream.readAllBytes()
+        and:
+        stream.close()
+        then:
+        noExceptionThrown()
+        and:
+        new String(result) == "Hello world"
+    }
+}
diff --git a/modules/nf-httpfs/src/test/nextflow/file/http/XFileSystemProviderTest.groovy b/modules/nf-httpfs/src/test/nextflow/file/http/XFileSystemProviderTest.groovy
index e5ea1add63..d64f7bd9c4 100644
--- a/modules/nf-httpfs/src/test/nextflow/file/http/XFileSystemProviderTest.groovy
+++ b/modules/nf-httpfs/src/test/nextflow/file/http/XFileSystemProviderTest.groovy
@@ -42,6 +42,7 @@ class XFileSystemProviderTest extends Specification {
 
     def "should return input stream from path"() {
         given:
+        def DATA = 'Hello world'
         def fsp = Spy(new HttpFileSystemProvider())
         def path = fsp.getPath(new URI('http://host.com/index.html?query=123'))
         def connection = Mock(URLConnection)
@@ -54,7 +55,8 @@ class XFileSystemProviderTest extends Specification {
             return connection
         }
         and:
-        connection.getInputStream() >> new ByteArrayInputStream('Hello world'.bytes)
+        connection.getInputStream() >> new ByteArrayInputStream(DATA.bytes)
+        connection.getContentLengthLong() >> DATA.size()
         and:
         stream.text == 'Hello world'
     }
diff --git a/nextflow b/nextflow
index 5fa211ed10..c89ca7617d 100755
--- a/nextflow
+++ b/nextflow
@@ -15,7 +15,7 @@
 #  limitations under the License.
 
 [[ "$NXF_DEBUG" == 'x' ]] && set -x
-NXF_VER=${NXF_VER:-'24.07.0-edge'}
+NXF_VER=${NXF_VER:-'24.11.0-edge'}
 NXF_ORG=${NXF_ORG:-'nextflow-io'}
 NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
 NXF_PROT=${NXF_PROT:-'https'}
@@ -313,7 +313,7 @@ if [ ! -x "$JAVA_CMD" ] ; then
             JAVA_CMD="$JAVA_HOME/bin/java"
         fi
     elif [ -x /usr/libexec/java_home ]; then
-        JAVA_CMD="$(/usr/libexec/java_home -v 11+ 2>/dev/null)/bin/java" || JAVA_CMD=java
+        JAVA_CMD="$(/usr/libexec/java_home -v 17+ 2>/dev/null)/bin/java" || JAVA_CMD=java
     else
         JAVA_CMD="$(which java)" || JAVA_CMD=java
     fi
@@ -344,14 +344,8 @@ else
   fi
   major=${BASH_REMATCH[1]}
   minor=${BASH_REMATCH[2]}
-  # legacy version - Java 7/8 only
-  if [ $major -eq 0 ] && [ $minor -lt 26 ]; then
-    version_check="^(1.7|1.8)"
-    version_message="Java 7 or 8"
-  else
-    version_check="^(1.8|9|10|11|12|13|14|15|16|17|18|19|20|21|22)"
-    version_message="Java 8 or later (up to 22)"
-  fi
+  version_check="^(17|18|19|20|21|22|23)"
+  version_message="Java 17 or later (up to 23)"
   if [[ ! $JAVA_VER =~ $version_check ]]; then
       echo_red "ERROR: Cannot find Java or it's a wrong version -- please make sure that $version_message is installed"
       if [[ "$NXF_JAVA_HOME" ]]; then
@@ -361,9 +355,6 @@ else
       fi
       exit 1
   fi
-  if [[ ! $JAVA_VER =~ ^(11|12|13|14|15|16|17|18|19|20|21|22) ]]; then
-      echo_yellow "NOTE: Nextflow is not tested with Java $JAVA_VER -- It's recommended the use of version 11 up to 22\n"
-  fi
   mkdir -p "$(dirname "$JAVA_KEY")"
   [[ -f $JAVA_VER ]] && echo $JAVA_VER > "$JAVA_KEY"
 fi
@@ -389,7 +380,6 @@ if [[ $NXF_LEGACY_LAUNCHER ]]; then
   [[ "$CAPSULE_LOG" ]] && JAVA_OPTS+=(-Dcapsule.log=$CAPSULE_LOG)
   [[ "$CAPSULE_RESET" ]] && JAVA_OPTS+=(-Dcapsule.reset=true)
 fi
-[[ "$JAVA_VER" =~ ^(21|22) ]] && [[ ! "$NXF_ENABLE_VIRTUAL_THREADS" ]] && NXF_ENABLE_VIRTUAL_THREADS=true
 [[ "$cmd" != "run" && "$cmd" != "node" ]] && JAVA_OPTS+=(-XX:+TieredCompilation -XX:TieredStopAtLevel=1)
 [[ "$NXF_OPTS" ]] && JAVA_OPTS+=($NXF_OPTS)
 [[ "$NXF_CLASSPATH" ]] && export NXF_CLASSPATH
@@ -462,33 +452,29 @@ else
     [[ "$NXF_JVM_ARGS" ]] && launcher+=($NXF_JVM_ARGS)
     [[ "$remote_debug" ]] && launcher+=(-agentlib:jdwp=transport=dt_socket,server=y,suspend=y,address=$NXF_REMOTE_DEBUG_PORT)
 
-    if [[ "$JAVA_VER" =~ ^(9|10|11|12|13|14|15|16|17|18|19|20|21|22) ]]; then
-      launcher+=(--add-opens=java.base/java.lang=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/java.io=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/java.nio=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/java.net=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/java.util=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/java.nio.file.spi=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/sun.nio.ch=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/sun.nio.fs=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/jdk.internal.vm=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/java.util.regex=ALL-UNNAMED)
-      if [[ "$NXF_ENABLE_VIRTUAL_THREADS" == 'true' ]]; then
-        if [[ "$JAVA_VER" =~ ^(19|20) ]]; then launcher+=(--enable-preview)
-        elif [[ ! "$JAVA_VER" =~ ^(21|22) ]]; then die "Virtual threads require Java 19 or later - current version $JAVA_VER"
-        fi
+    launcher+=(--add-opens=java.base/java.lang=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/java.io=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/java.nio=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/java.net=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/java.util=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/java.nio.file.spi=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/sun.nio.ch=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/sun.nio.fs=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/jdk.internal.vm=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/java.util.regex=ALL-UNNAMED)
+    if [[ "$NXF_ENABLE_VIRTUAL_THREADS" == 'true' ]]; then
+      if [[ "$JAVA_VER" =~ ^(19|20) ]]; then launcher+=(--enable-preview)
+      elif [[ ! "$JAVA_VER" =~ ^(21|22|23) ]]; then die "Virtual threads require Java 19 or later - current version $JAVA_VER"
       fi
-      launcher+=("${cmd_tail[@]}")
-    else
-      launcher+=("${cmd_tail[@]}")
     fi
+    launcher+=("${cmd_tail[@]}")
 
     # create the launch file only when using the legacy launcher (capsule)
     if [[ $NXF_LEGACY_LAUNCHER ]]; then
diff --git a/nextflow.md5 b/nextflow.md5
index 763bb14a5c..deb7f7a40a 100644
--- a/nextflow.md5
+++ b/nextflow.md5
@@ -1 +1 @@
-de590cf568c61fa941e4013d7f407902
+66995c4139ebcd17bf99f17d9dd030d1
diff --git a/nextflow.sha1 b/nextflow.sha1
index 36b7629f1e..ccadbdc25f 100644
--- a/nextflow.sha1
+++ b/nextflow.sha1
@@ -1 +1 @@
-3cc9902cd2713262f5fb29d652b749ef5676b3ed
+cdbb67bdb21c0e63fb48aabb8b168c12a31fa5b3
diff --git a/nextflow.sha256 b/nextflow.sha256
index b5f27a0a76..f4e9ccb3bd 100644
--- a/nextflow.sha256
+++ b/nextflow.sha256
@@ -1 +1 @@
-19515441f324cd32e272352b056d800293b639e1bfcc455257b4192115029831
+69a86852c52dcfa7662407c46d16f05bd3dec16e0c505c2a2f71ccc56219d631
diff --git a/packing.gradle b/packing.gradle
index f52825ed65..07e404c0d9 100644
--- a/packing.gradle
+++ b/packing.gradle
@@ -168,7 +168,7 @@ task installLauncher(type: Copy, dependsOn: ['pack']) {
 
 task installScratch(type: Copy, dependsOn: ['pack']) {
     from "$releaseDir/nextflow-$version-one.jar"
-    into "${rootProject.projectDir}/docker-scratch/.nextflow/framework/$version/"
+    into "${rootProject.projectDir}/test-e2e/.nextflow/framework/$version/"
 }
 
 /*
diff --git a/plugins/nf-amazon/build.gradle b/plugins/nf-amazon/build.gradle
index 08d2adccca..e8a8c75eeb 100644
--- a/plugins/nf-amazon/build.gradle
+++ b/plugins/nf-amazon/build.gradle
@@ -38,24 +38,27 @@ dependencies {
     compileOnly 'org.pf4j:pf4j:3.12.0'
 
     api ('javax.xml.bind:jaxb-api:2.4.0-b180830.0359')
-    api ('com.amazonaws:aws-java-sdk-s3:1.12.766')
-    api ('com.amazonaws:aws-java-sdk-ec2:1.12.766')
-    api ('com.amazonaws:aws-java-sdk-batch:1.12.766')
-    api ('com.amazonaws:aws-java-sdk-iam:1.12.766')
-    api ('com.amazonaws:aws-java-sdk-ecs:1.12.766')
-    api ('com.amazonaws:aws-java-sdk-logs:1.12.766')
-    api ('com.amazonaws:aws-java-sdk-codecommit:1.12.766')
-    api ('com.amazonaws:aws-java-sdk-sts:1.12.766')
-    api ('com.amazonaws:aws-java-sdk-ses:1.12.766')
+    api ('com.amazonaws:aws-java-sdk-s3:1.12.777')
+    api ('com.amazonaws:aws-java-sdk-ec2:1.12.777')
+    api ('com.amazonaws:aws-java-sdk-batch:1.12.777')
+    api ('com.amazonaws:aws-java-sdk-iam:1.12.777')
+    api ('com.amazonaws:aws-java-sdk-ecs:1.12.777')
+    api ('com.amazonaws:aws-java-sdk-logs:1.12.777')
+    api ('com.amazonaws:aws-java-sdk-codecommit:1.12.777')
+    api ('com.amazonaws:aws-java-sdk-sts:1.12.777')
+    api ('com.amazonaws:aws-java-sdk-ses:1.12.777')
     api ('software.amazon.awssdk:sso:2.26.26')
     api ('software.amazon.awssdk:ssooidc:2.26.26')
 
     constraints {
         api 'com.fasterxml.jackson.core:jackson-databind:2.12.7.1'
     }
+
+    // address security vulnerabilities
+    runtimeOnly 'io.netty:netty-common:4.1.115.Final'
         
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation project(':nextflow')
-    testImplementation "org.apache.groovy:groovy:4.0.22"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.22"
+    testImplementation "org.apache.groovy:groovy:4.0.24"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.24"
 }
diff --git a/plugins/nf-amazon/changelog.txt b/plugins/nf-amazon/changelog.txt
index 911ac7d8f1..d9fc1213e9 100644
--- a/plugins/nf-amazon/changelog.txt
+++ b/plugins/nf-amazon/changelog.txt
@@ -1,5 +1,21 @@
 nf-amazon changelog
 ===================
+2.10.0 - 3 Dec 2024
+- Detecting errors in data unstaging (#5345) [3c8e602d]
+- Prevent NPE with null AWS Batch response [12fc1d60]
+- Fix Fargate warning on memory check (#5475) [bdf0ad00]
+- Bump groovy 4.0.24 [dd71ad31]
+- Bump aws sdk 1.12.777 (#5458) [8bad0b4b]
+- Bump netty-common to version 4.1.115.Final [d1bbd3d0]
+
+2.9.0 - 2 Oct 2024
+- Add Platform workflow prefix in AWS Batch job names (#5318) [e2e test] [42dd4ba8]
+- Fix AWS spot attempts with zero value (#5331) [ci fast] [bac2da12]
+- Bump groovy 4.0.23 (#5303) [ci fast] [fe3e3ac7]
+
+2.8.0 - 4 Sep 2024
+- Disable AWS spot retry (#5215) [f28fcb25]
+
 2.7.0 - 5 Aug 2024
 - More robust parsing of shm-size containerOptions (#5177) [b56802a3]
 - Fix AWS Cloudwatch access when using custom log group name [30195838]
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy
index bf97bf976a..c96b6b33e5 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy
@@ -60,6 +60,7 @@ import groovy.transform.CompileStatic
 import groovy.transform.Memoized
 import groovy.util.logging.Slf4j
 import nextflow.BuildInfo
+import nextflow.SysEnv
 import nextflow.cloud.types.CloudMachineInfo
 import nextflow.container.ContainerNameValidator
 import nextflow.exception.ProcessException
@@ -112,7 +113,7 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
 
     private CloudMachineInfo machineInfo
 
-    private Map<String,String> environment
+    private Map<String,String> environment = Map<String,String>.of()
 
     final static private Map<String,String> jobDefinitions = [:]
 
@@ -134,7 +135,7 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
         super(task)
         this.executor = executor
         this.client = executor.client
-        this.environment = System.getenv()
+        this.environment = SysEnv.get()
         this.logFile = task.workDir.resolve(TaskRun.CMD_LOG)
         this.scriptFile = task.workDir.resolve(TaskRun.CMD_SCRIPT)
         this.inputFile =  task.workDir.resolve(TaskRun.CMD_INFILE)
@@ -198,7 +199,7 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
         // retrieve the status for the specified job and along with the next batch
         log.trace "[AWS BATCH] requesting describe jobs=${jobIdsToString(batchIds)}"
         DescribeJobsResult resp = client.describeJobs(new DescribeJobsRequest().withJobs(batchIds))
-        if( !resp.getJobs() ) {
+        if( !resp || !resp.getJobs() ) {
             log.debug "[AWS BATCH] cannot retrieve running status for job=$jobId"
             return null
         }
@@ -699,6 +700,11 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
         return executor.awsOptions.maxSpotAttempts
     }
 
+    protected String getJobName(TaskRun task) {
+        final result = prependWorkflowPrefix(task.name, environment)
+        return normalizeJobName(result)
+    }
+
     /**
      * Create a new Batch job request for the given NF {@link TaskRun}
      *
@@ -713,7 +719,7 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
         final opts = getAwsOptions()
         final labels = task.config.getResourceLabels()
         final result = new SubmitJobRequest()
-        result.setJobName(normalizeJobName(task.name))
+        result.setJobName(getJobName(task))
         result.setJobQueue(getJobQueue(task))
         result.setJobDefinition(getJobDefinition(task))
         if( labels ) {
@@ -839,11 +845,10 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
      * @return A job name without invalid characters
      */
     protected String normalizeJobName(String name) {
-        def result = name.replaceAll(' ','_').replaceAll(/[^a-zA-Z0-9_]/,'')
+        def result = name.replaceAll(' ','_').replaceAll(/[^a-zA-Z0-9_-]/,'')
         result.size()>128 ? result.substring(0,128) : result
     }
 
-
     protected CloudMachineInfo getMachineInfo() {
         if( machineInfo )
             return machineInfo
@@ -927,7 +932,7 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
         final slot = FARGATE_MEM.get(cpus)
         if( slot==null )
             throw new ProcessUnrecoverableException("Requirement of $cpus CPUs is not allowed by Fargate -- Check process with name '${task.lazyName()}'")
-        if( mega <=slot.min ) {
+        if( mega <slot.min ) {
             log.warn "Process '${task.lazyName()}' memory requirement of ${mem} is below the minimum allowed by Fargate of ${MemoryUnit.of(mega+'MB')}"
             return slot.min
         }
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsBatchConfig.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsBatchConfig.groovy
index e6e4cda964..24f376635f 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsBatchConfig.groovy
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsBatchConfig.groovy
@@ -36,7 +36,7 @@ import nextflow.util.Duration
 @CompileStatic
 class AwsBatchConfig implements CloudTransferOptions {
 
-    public static final int DEFAULT_MAX_SPOT_ATTEMPTS = 5
+    public static final int DEFAULT_MAX_SPOT_ATTEMPTS = 0
 
     public static final int DEFAULT_AWS_MAX_ATTEMPTS = 5
 
@@ -101,7 +101,7 @@ class AwsBatchConfig implements CloudTransferOptions {
         maxParallelTransfers = opts.maxParallelTransfers as Integer ?: MAX_TRANSFER
         maxTransferAttempts = opts.maxTransferAttempts as Integer ?: defaultMaxTransferAttempts()
         delayBetweenAttempts = opts.delayBetweenAttempts as Duration ?: DEFAULT_DELAY_BETWEEN_ATTEMPTS
-        maxSpotAttempts = opts.maxSpotAttempts as Integer ?: DEFAULT_MAX_SPOT_ATTEMPTS
+        maxSpotAttempts = opts.maxSpotAttempts!=null ? opts.maxSpotAttempts as Integer : DEFAULT_MAX_SPOT_ATTEMPTS
         volumes = makeVols(opts.volumes)
         jobRole = opts.jobRole
         logsGroup = opts.logsGroup
diff --git a/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF b/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
index 1e34af703f..7772ceb96b 100644
--- a/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.cloud.aws.AmazonPlugin
 Plugin-Id: nf-amazon
-Plugin-Version: 2.7.0
+Plugin-Version: 2.10.0
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=24.04.4
diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchTaskHandlerTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchTaskHandlerTest.groovy
index 2363152e02..44455a7a11 100644
--- a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchTaskHandlerTest.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchTaskHandlerTest.groovy
@@ -66,6 +66,7 @@ class AwsBatchTaskHandlerTest extends Specification {
         expect:
         handler.normalizeJobName('foo') == 'foo'
         handler.normalizeJobName('foo (12)') == 'foo_12'
+        handler.normalizeJobName('foo-12') == 'foo-12'
 
         when:
         def looong = '012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789'
@@ -98,7 +99,7 @@ class AwsBatchTaskHandlerTest extends Specification {
         1 * handler.getJobDefinition(task) >> 'job-def:1'
         1 * handler.getEnvironmentVars() >> [VAR_FOO, VAR_BAR]
 
-        req.getJobName() == 'batchtask'
+        req.getJobName() == 'batch-task'
         req.getJobQueue() == 'queue1'
         req.getJobDefinition() == 'job-def:1'
         req.getContainerOverrides().getResourceRequirements().find { it.type=='VCPU'}.getValue() == '4'
@@ -119,7 +120,7 @@ class AwsBatchTaskHandlerTest extends Specification {
         1 * handler.getJobDefinition(task) >> 'job-def:1'
         1 * handler.getEnvironmentVars() >> [VAR_FOO, VAR_BAR]
 
-        req.getJobName() == 'batchtask'
+        req.getJobName() == 'batch-task'
         req.getJobQueue() == 'queue1'
         req.getJobDefinition() == 'job-def:1'
         req.getContainerOverrides().getResourceRequirements().find { it.type=='VCPU'}.getValue() == '4'
@@ -149,7 +150,7 @@ class AwsBatchTaskHandlerTest extends Specification {
         1 * handler.getJobDefinition(task) >> 'job-def:1'
         1 * handler.getEnvironmentVars() >> []
 
-        req.getJobName() == 'batchtask'
+        req.getJobName() == 'batch-task'
         req.getJobQueue() == 'queue1'
         req.getJobDefinition() == 'job-def:1'
         req.getContainerOverrides().getResourceRequirements().find { it.type=='VCPU'}.getValue() == '4'
@@ -166,7 +167,7 @@ class AwsBatchTaskHandlerTest extends Specification {
         1 * handler.getJobDefinition(task) >> 'job-def:1'
         1 * handler.getEnvironmentVars() >> []
 
-        req2.getJobName() == 'batchtask'
+        req2.getJobName() == 'batch-task'
         req2.getJobQueue() == 'queue1'
         req2.getJobDefinition() == 'job-def:1'
         req2.getContainerOverrides().getResourceRequirements().find { it.type=='VCPU'}.getValue() == '4'
@@ -233,7 +234,7 @@ class AwsBatchTaskHandlerTest extends Specification {
         1 * handler.getJobQueue(task) >> 'queue1'
         1 * handler.getJobDefinition(task) >> 'job-def:1'
         and:
-        req.getJobName() == 'batchtask'
+        req.getJobName() == 'batch-task'
         req.getJobQueue() == 'queue1'
         req.getJobDefinition() == 'job-def:1'
         req.getTimeout() == null
@@ -250,7 +251,7 @@ class AwsBatchTaskHandlerTest extends Specification {
         1 * handler.getJobQueue(task) >> 'queue2'
         1 * handler.getJobDefinition(task) >> 'job-def:2'
         and:
-        req.getJobName() == 'batchtask'
+        req.getJobName() == 'batch-task'
         req.getJobQueue() == 'queue2'
         req.getJobDefinition() == 'job-def:2'
         // minimal allowed timeout is 60 seconds
@@ -269,7 +270,7 @@ class AwsBatchTaskHandlerTest extends Specification {
         1 * handler.getJobQueue(task) >> 'queue3'
         1 * handler.getJobDefinition(task) >> 'job-def:3'
         and:
-        req.getJobName() == 'batchtask'
+        req.getJobName() == 'batch-task'
         req.getJobQueue() == 'queue3'
         req.getJobDefinition() == 'job-def:3'
         // minimal allowed timeout is 60 seconds
@@ -300,7 +301,7 @@ class AwsBatchTaskHandlerTest extends Specification {
         1 * handler.getJobQueue(task) >> 'queue1'
         1 * handler.getJobDefinition(task) >> 'job-def:1'
         and:
-        req.getJobName() == 'batchtask'
+        req.getJobName() == 'batch-task'
         req.getJobQueue() == 'queue1'
         req.getJobDefinition() == 'job-def:1'
         // no error `retry` error strategy is defined by NF, use `maxRetries` to se Batch attempts
@@ -1014,7 +1015,7 @@ class AwsBatchTaskHandlerTest extends Specification {
         1 * handler.getJobDefinition(task) >> 'job-def:1'
         1 * handler.getEnvironmentVars() >> [VAR_FOO, VAR_BAR]
 
-        req.getJobName() == 'batchtask'
+        req.getJobName() == 'batch-task'
         req.getJobQueue() == 'queue1'
         req.getJobDefinition() == 'job-def:1'
         req.getContainerOverrides().getResourceRequirements().find { it.type=='VCPU'}.getValue() == '4'
@@ -1103,4 +1104,25 @@ class AwsBatchTaskHandlerTest extends Specification {
         'job1'       | 'job1'
         'job1:task2' | 'job1'
     }
+
+    def 'should get job name' () {
+        given:
+        def handler = Spy(new AwsBatchTaskHandler(environment: ENV))
+        def task = Mock(TaskRun)
+
+        when:
+        def result = handler.getJobName(task)
+        then:
+        task.getName() >> NAME
+        and:
+        result == EXPECTED
+        
+        where:
+        ENV                             | NAME      | EXPECTED
+        [:]                             | 'foo'     | 'foo'
+        [TOWER_WORKFLOW_ID: '12345']    | 'foo'     | 'tw-12345-foo'
+        [TOWER_WORKFLOW_ID: '12345']    | 'foo'     | 'tw-12345-foo'
+        [TOWER_WORKFLOW_ID: '12345']    | 'foo(12)' | 'tw-12345-foo12'
+
+    }
 }
diff --git a/plugins/nf-amazon/src/test/nextflow/executor/BashWrapperBuilderWithS3Test.groovy b/plugins/nf-amazon/src/test/nextflow/executor/BashWrapperBuilderWithS3Test.groovy
index 3e213444cb..4f90e22aa2 100644
--- a/plugins/nf-amazon/src/test/nextflow/executor/BashWrapperBuilderWithS3Test.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/executor/BashWrapperBuilderWithS3Test.groovy
@@ -58,7 +58,7 @@ class BashWrapperBuilderWithS3Test extends Specification {
         binding.unstage_outputs == '''\
                     IFS=$'\\n'
                     for name in $(eval "ls -1d test.bam test.bai bla\\ nk.txt" | sort | uniq); do
-                        nxf_s3_upload $name s3://some/buck\\ et || true
+                        nxf_s3_upload $name s3://some/buck\\ et
                     done
                     unset IFS
                     '''.stripIndent().rightTrim()
diff --git a/plugins/nf-azure/build.gradle b/plugins/nf-azure/build.gradle
index adee9807e5..2116355076 100644
--- a/plugins/nf-azure/build.gradle
+++ b/plugins/nf-azure/build.gradle
@@ -43,12 +43,15 @@ dependencies {
         exclude group: 'org.slf4j', module: 'slf4j-api'
         exclude group: 'com.google.guava', module: 'guava'
     }
-    api('com.azure:azure-identity:1.11.3') {
+    api('com.azure:azure-identity:1.12.2') {
         exclude group: 'org.slf4j', module: 'slf4j-api'
     }
 
+    // address security vulnerabilities
+    runtimeOnly 'io.netty:netty-common:4.1.115.Final'
+
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation project(':nextflow')
-    testImplementation "org.apache.groovy:groovy:4.0.22"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.22"
+    testImplementation "org.apache.groovy:groovy:4.0.24"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.24"
 }
diff --git a/plugins/nf-azure/changelog.txt b/plugins/nf-azure/changelog.txt
index 3fba12494f..780fda1082 100644
--- a/plugins/nf-azure/changelog.txt
+++ b/plugins/nf-azure/changelog.txt
@@ -1,5 +1,22 @@
 nf-azure changelog
 ===================
+1.11.0 - 3 Dec 2024
+- Detecting errors in data unstaging (#5345) [3c8e602d]
+- Bump netty-common to version 4.1.115.Final [d1bbd3d0]
+- Bump groovy 4.0.24 [dd71ad31]
+- Bump com.azure:azure-identity from 1.11.3 to 1.12.2 (#5449) [cb70f1df]
+- Target Java 17 as minimal Java version (#5045) [0140f954]
+
+1.10.1 - 27 Oct 2024
+- Demote azure batch task status log level to trace (#5416) [ci skip] [d6c684bb]
+
+1.10.0 - 2 Oct 2024
+- Fix Azure Fusion env misses credentials when no key or SAS provided (#5328) [e11382c8]
+- Bump groovy 4.0.23 (#5303) [ci fast] [fe3e3ac7]
+
+1.9.0 - 4 Sep 2024
+- Support Azure Managed Identities in Fusion configuration logic (#5278) [a0bf8b40]
+
 1.8.1 - 5 Aug 2024
 - Bump pf4j to version 3.12.0 [96117b9a]
 
diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy
index 7aa7a1430e..b359a87cb7 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy
@@ -98,7 +98,7 @@ class AzBatchTaskHandler extends TaskHandler implements FusionAwareTask {
         // note, include complete status otherwise it hangs if the task
         // completes before reaching this check
         final running = state==BatchTaskState.RUNNING || state==BatchTaskState.COMPLETED
-        log.debug "[AZURE BATCH] Task status $task.name taskId=$taskKey; running=$running"
+        log.trace "[AZURE BATCH] Task status $task.name taskId=$taskKey; running=$running"
         if( running )
             this.status = TaskStatus.RUNNING
         return running
diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzActiveDirectoryOpts.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzActiveDirectoryOpts.groovy
index 462c6c8203..bc05264806 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzActiveDirectoryOpts.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzActiveDirectoryOpts.groovy
@@ -16,6 +16,7 @@
 package nextflow.cloud.azure.config
 
 import groovy.transform.CompileStatic
+import nextflow.SysEnv
 import nextflow.cloud.azure.nio.AzFileSystemProvider
 
 /**
@@ -26,18 +27,15 @@ import nextflow.cloud.azure.nio.AzFileSystemProvider
 @CompileStatic
 class AzActiveDirectoryOpts {
 
-    private Map<String, String> sysEnv
-
     String servicePrincipalId
     String servicePrincipalSecret
     String tenantId
 
     AzActiveDirectoryOpts(Map config, Map<String, String> env = null) {
         assert config != null
-        this.sysEnv = env == null ? new HashMap<String, String>(System.getenv()) : env
-        this.servicePrincipalId = config.servicePrincipalId ?: sysEnv.get('AZURE_CLIENT_ID')
-        this.servicePrincipalSecret = config.servicePrincipalSecret ?: sysEnv.get('AZURE_CLIENT_SECRET')
-        this.tenantId = config.tenantId ?: sysEnv.get('AZURE_TENANT_ID')
+        this.servicePrincipalId = config.servicePrincipalId ?: SysEnv.get('AZURE_CLIENT_ID')
+        this.servicePrincipalSecret = config.servicePrincipalSecret ?: SysEnv.get('AZURE_CLIENT_SECRET')
+        this.tenantId = config.tenantId ?: SysEnv.get('AZURE_TENANT_ID')
     }
 
     Map<String, Object> getEnv() {
diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzRegistryOpts.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzRegistryOpts.groovy
index 16bb25548b..386571cf2d 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzRegistryOpts.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzRegistryOpts.groovy
@@ -16,8 +16,8 @@
 
 package nextflow.cloud.azure.config
 
-
 import groovy.transform.CompileStatic
+import nextflow.SysEnv
 
 /**
  * Model Azure Batch registry config settings from nextflow config file
@@ -27,8 +27,6 @@ import groovy.transform.CompileStatic
 @CompileStatic
 class AzRegistryOpts {
 
-    private Map<String,String> sysEnv
-
     String server
     String userName
     String password
@@ -37,12 +35,11 @@ class AzRegistryOpts {
         this(Collections.emptyMap())
     }
 
-    AzRegistryOpts(Map config, Map<String,String> env=null) {
+    AzRegistryOpts(Map config, Map<String,String> env=SysEnv.get()) {
         assert config!=null
-        this.sysEnv = env==null ? new HashMap<String,String>(System.getenv()) : env
         this.server = config.server ?: 'docker.io'
-        this.userName = config.userName ?: sysEnv.get('AZURE_REGISTRY_USER_NAME')
-        this.password = config.password ?: sysEnv.get('AZURE_REGISTRY_PASSWORD')
+        this.userName = config.userName ?: env.get('AZURE_REGISTRY_USER_NAME')
+        this.password = config.password ?: env.get('AZURE_REGISTRY_PASSWORD')
     }
 
     boolean isConfigured() {
diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzStorageOpts.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzStorageOpts.groovy
index 1bfecfb780..d3e6bb3259 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzStorageOpts.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzStorageOpts.groovy
@@ -17,6 +17,7 @@
 package nextflow.cloud.azure.config
 
 import groovy.transform.CompileStatic
+import nextflow.SysEnv
 import nextflow.cloud.azure.batch.AzHelper
 import nextflow.cloud.azure.nio.AzFileSystemProvider
 import nextflow.util.Duration
@@ -28,7 +29,6 @@ import nextflow.util.Duration
 @CompileStatic
 class AzStorageOpts {
 
-    private Map<String,String> sysEnv
     String accountKey
     String accountName
     String sasToken
@@ -36,12 +36,11 @@ class AzStorageOpts {
     Map<String,AzFileShareOpts> fileShares
 
 
-    AzStorageOpts(Map config, Map<String,String> env=null) {
+    AzStorageOpts(Map config, Map<String,String> env=SysEnv.get()) {
         assert config!=null
-        this.sysEnv = env==null ? new HashMap<String,String>(System.getenv()) : env
-        this.accountKey = config.accountKey ?: sysEnv.get('AZURE_STORAGE_ACCOUNT_KEY')
-        this.accountName = config.accountName ?: sysEnv.get('AZURE_STORAGE_ACCOUNT_NAME')
-        this.sasToken = config.sasToken ?: sysEnv.get('AZURE_STORAGE_SAS_TOKEN')
+        this.accountKey = config.accountKey ?: env.get('AZURE_STORAGE_ACCOUNT_KEY')
+        this.accountName = config.accountName ?: env.get('AZURE_STORAGE_ACCOUNT_NAME')
+        this.sasToken = config.sasToken ?: env.get('AZURE_STORAGE_SAS_TOKEN')
         this.tokenDuration = (config.tokenDuration as Duration) ?: Duration.of('48h')
         this.fileShares = parseFileShares(config.fileShares instanceof Map ? config.fileShares as Map<String, Map>
                 : Collections.<String,Map> emptyMap())
@@ -63,10 +62,4 @@ class AzStorageOpts {
         }
         return result
     }
-
-    synchronized String getOrCreateSasToken() {
-        if( !sasToken )
-            sasToken = AzHelper.generateAccountSas(accountName, accountKey, tokenDuration)
-        return sasToken
-    }
 }
diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/fusion/AzFusionEnv.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/fusion/AzFusionEnv.groovy
index 188e411c29..a4b9e8e344 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/fusion/AzFusionEnv.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/fusion/AzFusionEnv.groovy
@@ -17,34 +17,72 @@
 
 package nextflow.cloud.azure.fusion
 
+import groovy.util.logging.Slf4j
+import nextflow.Global
+import nextflow.cloud.azure.batch.AzHelper
 import groovy.transform.CompileStatic
 import nextflow.cloud.azure.config.AzConfig
 import nextflow.fusion.FusionConfig
 import nextflow.fusion.FusionEnv
 import org.pf4j.Extension
+
 /**
  * Implement environment provider for Azure specific variables
- * 
+ *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
 @Extension
 @CompileStatic
+@Slf4j
 class AzFusionEnv implements FusionEnv {
 
     @Override
     Map<String, String> getEnvironment(String scheme, FusionConfig config) {
-        if( scheme!='az' )
-            return Collections.<String,String>emptyMap()
+        if (scheme != 'az') {
+            return Collections.<String, String> emptyMap()
+        }
 
-        final cfg = AzConfig.config.storage()
+        final cfg = AzConfig.config
         final result = new LinkedHashMap(10)
-        if( !cfg.accountName )
-            throw new IllegalArgumentException("Missing Azure storage account name")
-        if( !cfg.sasToken && !cfg.accountKey )
-            throw new IllegalArgumentException("Missing Azure storage SAS token")
-        
-        result.AZURE_STORAGE_ACCOUNT = cfg.accountName
-        result.AZURE_STORAGE_SAS_TOKEN = cfg.getOrCreateSasToken()
+
+        if (!cfg.storage().accountName) {
+            throw new IllegalArgumentException("Missing Azure Storage account name")
+        }
+
+        if (cfg.storage().accountKey && cfg.storage().sasToken) {
+            throw new IllegalArgumentException("Azure Storage Access key and SAS token detected. Only one is allowed")
+        }
+
+        result.AZURE_STORAGE_ACCOUNT = cfg.storage().accountName
+        // In theory, generating an impromptu SAS token for authentication methods other than
+        // `azure.storage.sasToken` should not be necessary, because those methods should already allow sufficient
+        // access for normal operation. Nevertheless, #5287 heavily implies that failing to do so causes the Azure
+        // Storage plugin or Fusion to fail. In any case, it may be possible to remove this in the future.
+        result.AZURE_STORAGE_SAS_TOKEN = getOrCreateSasToken()
+
         return result
     }
+
+    /**
+     * Return the SAS token if it is defined in the configuration, otherwise generate one based on the requested
+     * authentication method.
+     */
+    synchronized String getOrCreateSasToken() {
+
+        final cfg = AzConfig.config
+
+        // If a SAS token is already defined in the configuration, just return it
+        if (cfg.storage().sasToken) {
+            return cfg.storage().sasToken
+        }
+
+        // For Active Directory and Managed Identity, we cannot generate an *account* SAS token, but we can generate
+        // a *container* SAS token for the work directory.
+        if (cfg.activeDirectory().isConfigured() || cfg.managedIdentity().isConfigured()) {
+            return AzHelper.generateContainerSasWithActiveDirectory(Global.session.workDir, cfg.storage().tokenDuration)
+        }
+
+        // Shared Key authentication can use an account SAS token
+        return AzHelper.generateAccountSasWithAccountKey(Global.session.workDir, cfg.storage().tokenDuration)
+    }
 }
diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/nio/AzFileSystem.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/nio/AzFileSystem.groovy
index e890dbb559..41a1b62d4a 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/nio/AzFileSystem.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/nio/AzFileSystem.groovy
@@ -527,8 +527,15 @@ class AzFileSystem extends FileSystem {
      * @param cond A predicate that determines when a retry should be triggered
      * @return The {@link dev.failsafe.RetryPolicy} instance
      */
-    @Memoized
     protected <T> RetryPolicy<T> retryPolicy(Predicate<? extends Throwable> cond) {
+        // this is needed because apparently bytebuddy used by testing framework is not able
+        // to handle properly this method signature using both generics and `@Memoized` annotation.
+        // therefore the `@Memoized` has been moved to the inner method invocation
+        return (RetryPolicy<T>) retryPolicy0(cond)
+    }
+
+    @Memoized
+    protected RetryPolicy retryPolicy0(Predicate<? extends Throwable> cond) {
         final cfg = AzConfig.getConfig().retryConfig()
         final listener = new EventListener<ExecutionAttemptedEvent>() {
             @Override
@@ -536,7 +543,7 @@ class AzFileSystem extends FileSystem {
                 log.debug("Azure I/O exception - attempt: ${event.attemptCount}; cause: ${event.lastFailure?.message}")
             }
         }
-        return RetryPolicy.<T>builder()
+        return RetryPolicy.builder()
                 .handleIf(cond)
                 .withBackoff(cfg.delay.toMillis(), cfg.maxDelay.toMillis(), ChronoUnit.MILLIS)
                 .withMaxAttempts(cfg.maxAttempts)
diff --git a/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF b/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF
index 939940fc14..1ebcbf274f 100644
--- a/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.cloud.azure.AzurePlugin
 Plugin-Id: nf-azure
-Plugin-Version: 1.8.1
+Plugin-Version: 1.11.0
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=24.04.4
diff --git a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy
index 660291859a..eceeb644b2 100644
--- a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy
+++ b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy
@@ -10,6 +10,7 @@ import com.azure.identity.ManagedIdentityCredential
 import com.google.common.hash.HashCode
 import nextflow.Global
 import nextflow.Session
+import nextflow.SysEnv
 import nextflow.cloud.azure.config.AzConfig
 import nextflow.cloud.azure.config.AzManagedIdentityOpts
 import nextflow.cloud.azure.config.AzPoolOpts
@@ -31,6 +32,14 @@ class AzBatchServiceTest extends Specification {
 
     static long _1GB = 1024 * 1024 * 1024
 
+    def setup() {
+        SysEnv.push([:])  // <-- clear the system host env
+    }
+
+    def cleanup() {
+        SysEnv.pop()      // <-- restore the system host env
+    }
+
     def 'should make job id'() {
         given:
         def task = Mock(TaskRun) {
diff --git a/plugins/nf-azure/src/test/nextflow/cloud/azure/fusion/AzFusionEnvTest.groovy b/plugins/nf-azure/src/test/nextflow/cloud/azure/fusion/AzFusionEnvTest.groovy
new file mode 100644
index 0000000000..79774e9a9a
--- /dev/null
+++ b/plugins/nf-azure/src/test/nextflow/cloud/azure/fusion/AzFusionEnvTest.groovy
@@ -0,0 +1,199 @@
+/*
+ * Copyright 2013-2024, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.cloud.azure.fusion
+
+import nextflow.Global
+import nextflow.Session
+import nextflow.SysEnv
+import nextflow.fusion.FusionConfig
+
+import spock.lang.Specification
+
+/**
+ *
+ * @author Alberto Miranda <alberto.miranda@seqera.io>
+ */
+class AzFusionEnvTest extends Specification {
+
+    def setup() {
+        SysEnv.push([:])  // <-- clear the system host env
+    }
+
+    def cleanup() {
+        SysEnv.pop()      // <-- restore the system host env
+    }
+
+    def 'should return empty env'() {
+        given:
+        def provider = new AzFusionEnv()
+        when:
+        def env = provider.getEnvironment('aws', Mock(FusionConfig))
+        then:
+        env == Collections.emptyMap()
+    }
+
+    def 'should return env environment with SAS token config when accountKey is provided'() {
+        given:
+        def NAME = 'myaccount'
+        def KEY = 'myaccountkey'
+        Global.session = Mock(Session) {
+            getConfig() >> [azure: [storage: [accountName: NAME, accountKey: KEY]]]
+        }
+
+        when:
+        def config = Mock(FusionConfig)
+        def fusionEnv = Spy(AzFusionEnv)
+        1 * fusionEnv.getOrCreateSasToken() >> 'generatedSasToken'
+        def env = fusionEnv.getEnvironment('az', config)
+
+        then:
+        env.AZURE_STORAGE_ACCOUNT == NAME
+        env.AZURE_STORAGE_SAS_TOKEN
+        env.size() == 2
+    }
+
+    def 'should return env environment with SAS token config when a Service Principal is provided'() {
+        given:
+        def NAME = 'myaccount'
+        def CLIENT_ID = 'myclientid'
+        def CLIENT_SECRET = 'myclientsecret'
+        def TENANT_ID = 'mytenantid'
+        Global.session = Mock(Session) {
+            getConfig() >> [
+                azure: [
+                    activeDirectory: [
+                        servicePrincipalId: CLIENT_ID,
+                        servicePrincipalSecret: CLIENT_SECRET,
+                        tenantId: TENANT_ID
+                    ],
+                    storage: [
+                        accountName: NAME
+                    ]
+                ]
+            ]
+        }
+
+        when:
+        def config = Mock(FusionConfig)
+        def fusionEnv = Spy(AzFusionEnv)
+        1 * fusionEnv.getOrCreateSasToken() >> 'generatedSasToken'
+        def env = fusionEnv.getEnvironment('az', config)
+
+        then:
+        env.AZURE_STORAGE_ACCOUNT == NAME
+        env.AZURE_STORAGE_SAS_TOKEN == 'generatedSasToken'
+        env.size() == 2
+    }
+
+    def 'should return env environment with SAS token config when a user-assigned Managed Identity is provided'() {
+        given:
+        def NAME = 'myaccount'
+        def CLIENT_ID = 'myclientid'
+        Global.session = Mock(Session) {
+            getConfig() >> [
+                azure: [
+                    managedIdentity: [
+                        clientId: CLIENT_ID,
+                    ],
+                    storage: [
+                        accountName: NAME
+                    ]
+                ]
+            ]
+        }
+
+        when:
+        def config = Mock(FusionConfig)
+        def fusionEnv = Spy(AzFusionEnv)
+        1 * fusionEnv.getOrCreateSasToken() >> 'generatedSasToken'
+        def env = fusionEnv.getEnvironment('az', config)
+
+        then:
+        env.AZURE_STORAGE_ACCOUNT == NAME
+        env.AZURE_STORAGE_SAS_TOKEN == 'generatedSasToken'
+        env.size() == 2
+    }
+
+    def 'should return env environment with SAS token config when a system-assigned Managed Identity is provided'() {
+        given:
+        def NAME = 'myaccount'
+        Global.session = Mock(Session) {
+            getConfig() >> [
+                azure: [
+                    managedIdentity: [
+                        system: true
+                    ],
+                    storage: [
+                        accountName: NAME
+                    ]
+                ]
+            ]
+        }
+
+        when:
+        def config = Mock(FusionConfig)
+        def fusionEnv = Spy(AzFusionEnv)
+        1 * fusionEnv.getOrCreateSasToken() >> 'generatedSasToken'
+        def env = fusionEnv.getEnvironment('az', config)
+
+        then:
+        env.AZURE_STORAGE_ACCOUNT == NAME
+        env.AZURE_STORAGE_SAS_TOKEN == 'generatedSasToken'
+        env.size() == 2
+    }
+
+    def 'should return env environment with SAS token config when a sasToken is provided'() {
+        given:
+        Global.session = Mock(Session) {
+            getConfig() >> [azure: [storage: [accountName: 'x1', sasToken: 'y1']]]
+        }
+        and:
+
+        when:
+        def config = Mock(FusionConfig)
+        def env = new AzFusionEnv().getEnvironment('az', config)
+        then:
+        env == [AZURE_STORAGE_ACCOUNT: 'x1', AZURE_STORAGE_SAS_TOKEN: 'y1']
+
+    }
+
+    def 'should throw an exception when missing Azure Storage account name'() {
+        given:
+        Global.session = Mock(Session) {
+            getConfig() >> [azure: [storage: [sasToken: 'y1']]]
+        }
+        when:
+        def config = Mock(FusionConfig)
+        def env = new AzFusionEnv().getEnvironment('az', Mock(FusionConfig))
+        then:
+        thrown(IllegalArgumentException)
+    }
+
+    def 'should throw an exception when both account key and SAS token are present'() {
+        given:
+        Global.session = Mock(Session) {
+            getConfig() >> [azure: [storage: [accountName: 'x1', accountKey: 'y1', sasToken: 'z1']]]
+        }
+        when:
+        def config = Mock(FusionConfig)
+        def env = new AzFusionEnv().getEnvironment('az', Mock(FusionConfig))
+        then:
+        thrown(IllegalArgumentException)
+    }
+
+}
diff --git a/plugins/nf-azure/src/test/nextflow/executor/BashWrapperBuilderWithAzTest.groovy b/plugins/nf-azure/src/test/nextflow/executor/BashWrapperBuilderWithAzTest.groovy
index eb72d25163..1969345af5 100644
--- a/plugins/nf-azure/src/test/nextflow/executor/BashWrapperBuilderWithAzTest.groovy
+++ b/plugins/nf-azure/src/test/nextflow/executor/BashWrapperBuilderWithAzTest.groovy
@@ -47,7 +47,7 @@ class BashWrapperBuilderWithAzTest extends Specification {
         binding.unstage_outputs == """\
                     IFS=\$'\\n'
                     for name in \$(eval "ls -1d test.bam test.bai" | sort | uniq); do
-                        nxf_az_upload \$name '${AzHelper.toHttpUrl(target)}' || true
+                        nxf_az_upload \$name '${AzHelper.toHttpUrl(target)}'
                     done
                     unset IFS
                     """.stripIndent().rightTrim()
diff --git a/plugins/nf-cloudcache/build.gradle b/plugins/nf-cloudcache/build.gradle
index 8bd3fcc870..7cfa07de4b 100644
--- a/plugins/nf-cloudcache/build.gradle
+++ b/plugins/nf-cloudcache/build.gradle
@@ -35,7 +35,7 @@ dependencies {
     compileOnly 'org.pf4j:pf4j:3.12.0'
 
     testImplementation(testFixtures(project(":nextflow")))
-    testImplementation "org.apache.groovy:groovy:4.0.22"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.22"
+    testImplementation "org.apache.groovy:groovy:4.0.24"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.24"
 }
 
diff --git a/plugins/nf-codecommit/build.gradle b/plugins/nf-codecommit/build.gradle
index 8ae6e2e2cc..b0f16607e6 100644
--- a/plugins/nf-codecommit/build.gradle
+++ b/plugins/nf-codecommit/build.gradle
@@ -38,10 +38,10 @@ dependencies {
     compileOnly 'org.pf4j:pf4j:3.12.0'
 
     api ('javax.xml.bind:jaxb-api:2.4.0-b180830.0359')
-    api ('com.amazonaws:aws-java-sdk-codecommit:1.12.766')
+    api ('com.amazonaws:aws-java-sdk-codecommit:1.12.777')
         
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation project(':nextflow')
-    testImplementation "org.apache.groovy:groovy:4.0.22"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.22"
+    testImplementation "org.apache.groovy:groovy:4.0.24"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.24"
 }
diff --git a/plugins/nf-console/build.gradle b/plugins/nf-console/build.gradle
index e84430a4c1..64184c2b80 100644
--- a/plugins/nf-console/build.gradle
+++ b/plugins/nf-console/build.gradle
@@ -38,13 +38,13 @@ dependencies {
     compileOnly 'org.pf4j:pf4j:3.12.0'
 
     api("org.apache.groovy:groovy-console:4.0.21-patch.2") { transitive=false }
-    api("org.apache.groovy:groovy-swing:4.0.22")  { transitive=false }
+    api("org.apache.groovy:groovy-swing:4.0.24")  { transitive=false }
     // this is required by 'groovy-console'  
     api("com.github.javaparser:javaparser-core:3.25.8")
 
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation project(':nextflow')
-    testImplementation "org.apache.groovy:groovy:4.0.22"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.22"
+    testImplementation "org.apache.groovy:groovy:4.0.24"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.24"
 }
 
diff --git a/plugins/nf-google/build.gradle b/plugins/nf-google/build.gradle
index 9b768f8c57..954d4963ea 100644
--- a/plugins/nf-google/build.gradle
+++ b/plugins/nf-google/build.gradle
@@ -39,15 +39,15 @@ dependencies {
 
     api 'com.google.apis:google-api-services-lifesciences:v2beta-rev20210527-1.31.5'
     api 'com.google.auth:google-auth-library-oauth2-http:0.18.0'
-    api 'com.google.cloud:google-cloud-batch:0.29.0'
-    api 'com.google.cloud:google-cloud-logging:3.8.0'
+    api 'com.google.cloud:google-cloud-batch:0.53.0'
+    api 'com.google.cloud:google-cloud-logging:3.20.6'
     api 'com.google.cloud:google-cloud-nio:0.124.8'
     api 'com.google.cloud:google-cloud-storage:2.9.3'
     api 'com.google.code.gson:gson:2.10.1'
 
     testImplementation(testFixtures(project(":nextflow")))
-    testImplementation "org.apache.groovy:groovy:4.0.22"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.22"
+    testImplementation "org.apache.groovy:groovy:4.0.24"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.24"
 }
 
 test {
diff --git a/plugins/nf-google/changelog.txt b/plugins/nf-google/changelog.txt
index 5b8a54a4dc..f7d23811e6 100644
--- a/plugins/nf-google/changelog.txt
+++ b/plugins/nf-google/changelog.txt
@@ -1,5 +1,23 @@
 nf-google changelog
 ===================
+1.16.0 - 3 Dec 2024
+- Detecting errors in data unstaging (#5345) [3c8e602d]
+- Bump bouncycastle to jdk18on:1.78.1  (#5467) [cd8c385f]
+- Bump groovy 4.0.24 [dd71ad31]
+- Bump protobuf-java:3.25.5 to nf-google [488b7906]
+- Add NotFoundException to retry condition for Google Batch [aa4d19cc]
+
+1.15.2 - 14 Oct 2024
+- Add Google LS deprecation notice (#5400) [0ee1d9bc]
+
+1.15.1 - 13 Oct 2024
+- Add retry policy to google batch describe task (#5356) [64bb5a92]
+
+1.15.0 - 4 Sep 2024
+- Add Google Batch warning when for conflicting disk image config (#5279) [ci fast] [96cb57cb]
+- Add support for Google Batch used specified boot images  (#5268) [0aaa6482]
+- Disable Google Batch automatic spot retries (#5223) [aad21533]
+
 1.14.0 - 5 Aug 2024
 - Bump pf4j to version 3.12.0 [96117b9a]
 - Make Google Batch auto retry codes configurable (#5148) [e562ce06]
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
index f897438b1c..b965c5d8c9 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
@@ -61,7 +61,9 @@ import nextflow.util.TestOnly
 @CompileStatic
 class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
 
-    private static Pattern EXIT_CODE_REGEX = ~/exit code 500(\d\d)/
+    private static final Pattern EXIT_CODE_REGEX = ~/exit code 500(\d\d)/
+
+    private static final Pattern BATCH_ERROR_REGEX = ~/Batch Error: code/
 
     private GoogleBatchExecutor executor
 
@@ -99,6 +101,11 @@ class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
 
     private volatile long timestamp
 
+    /**
+     * A flag to indicate that the job has failed without launching any tasks
+     */
+    private volatile boolean noTaskJobfailure
+
     GoogleBatchTaskHandler(TaskRun task, GoogleBatchExecutor executor) {
         super(task)
         this.client = executor.getClient()
@@ -302,6 +309,9 @@ class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
             if( task.config.getDisk() )
                 log.warn1 'Process directive `disk` ignored because an instance template was specified'
 
+            if( executor.config.getBootDiskImage() )
+                log.warn1 'Config option `google.batch.bootDiskImage` ignored because an instance template was specified'
+
             if( executor.config.cpuPlatform )
                 log.warn1 'Config option `google.batch.cpuPlatform` ignored because an instance template was specified'
 
@@ -331,6 +341,9 @@ class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
                 instancePolicyOrTemplate.setInstallGpuDrivers(true)
             }
 
+            if( executor.config.getBootDiskImage() )
+                instancePolicy.setBootDisk( AllocationPolicy.Disk.newBuilder().setImage( executor.config.getBootDiskImage() ) )
+
             if( fusionEnabled() && !disk ) {
                 disk = new DiskResource(request: '375 GB', type: 'local-ssd')
                 log.debug "[GOOGLE BATCH] Process `${task.lazyName()}` - adding local volume as fusion scratch: $disk"
@@ -438,9 +451,10 @@ class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
      */
     protected String getTaskState() {
         final tasks = client.listTasks(jobId)
-        if( !tasks.iterator().hasNext() )
-            return 'PENDING'
-
+        if( !tasks.iterator().hasNext() ) {
+            // if there are no tasks checks the job status
+            return checkJobStatus()
+        }
         final now = System.currentTimeMillis()
         final delta =  now - timestamp;
         if( !taskState || delta >= 1_000) {
@@ -461,6 +475,21 @@ class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
         return taskState
     }
 
+    protected String checkJobStatus() {
+        final jobStatus = client.getJobStatus(jobId)
+        final newState = jobStatus?.state as String
+        if (newState) {
+            taskState = newState
+            timestamp = System.currentTimeMillis()
+            if (newState == "FAILED") {
+                noTaskJobfailure = true
+            }
+            return taskState
+        } else {
+            return "PENDING"
+        }
+    }
+
     static private final List<String> RUNNING_OR_COMPLETED = ['RUNNING', 'SUCCEEDED', 'FAILED']
 
     static private final List<String> COMPLETED = ['SUCCEEDED', 'FAILED']
@@ -503,13 +532,14 @@ class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
 
     protected Throwable getJobError() {
         try {
-            final status = client.getTaskStatus(jobId, taskId)
-            final eventsCount = status.getStatusEventsCount()
-            final lastEvent = eventsCount > 0 ? status.getStatusEvents(eventsCount - 1) : null
+            final events = noTaskJobfailure
+                ? client.getJobStatus(jobId).getStatusEventsList()
+                : client.getTaskStatus(jobId, taskId).getStatusEventsList()
+            final lastEvent = events?.get(events.size() - 1)
             log.debug "[GOOGLE BATCH] Process `${task.lazyName()}` - last event: ${lastEvent}; exit code: ${lastEvent?.taskExecution?.exitCode}"
 
             final error = lastEvent?.description
-            if( error && EXIT_CODE_REGEX.matcher(error).find() ) {
+            if( error && (EXIT_CODE_REGEX.matcher(error).find() || BATCH_ERROR_REGEX.matcher(error).find()) ) {
                 return new ProcessException(error)
             }
         }
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchClient.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchClient.groovy
index 7c0fe3cfb7..ffc3da905a 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchClient.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchClient.groovy
@@ -22,12 +22,14 @@ import java.util.function.Predicate
 
 import com.google.api.gax.core.CredentialsProvider
 import com.google.api.gax.rpc.FixedHeaderProvider
+import com.google.api.gax.rpc.NotFoundException
 import com.google.api.gax.rpc.UnavailableException
 import com.google.auth.Credentials
 import com.google.cloud.batch.v1.BatchServiceClient
 import com.google.cloud.batch.v1.BatchServiceSettings
 import com.google.cloud.batch.v1.Job
 import com.google.cloud.batch.v1.JobName
+import com.google.cloud.batch.v1.JobStatus
 import com.google.cloud.batch.v1.LocationName
 import com.google.cloud.batch.v1.Task
 import com.google.cloud.batch.v1.TaskGroupName
@@ -107,7 +109,7 @@ class BatchClient {
 
     Task describeTask(String jobId, String taskId) {
         final name = TaskName.of(projectId, location, jobId, 'group0', taskId)
-        return batchServiceClient.getTask(name)
+        return apply(()-> batchServiceClient.getTask(name))
     }
 
     void deleteJob(String jobId) {
@@ -119,6 +121,10 @@ class BatchClient {
         return describeTask(jobId, taskId).getStatus()
     }
 
+    JobStatus getJobStatus(String jobId) {
+        return describeJob(jobId).getStatus()
+    }
+
     String getTaskState(String jobId, String taskId) {
         final status = getTaskStatus(jobId, taskId)
         return status ? status.getState().toString() : null
@@ -175,6 +181,8 @@ class BatchClient {
                     return true
                 if( t instanceof TimeoutException || t.cause instanceof TimeoutException )
                     return true
+                if( t instanceof NotFoundException || t.cause instanceof NotFoundException )
+                    return true
                 return false
             }
         }
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy
index 6af5c0abb0..de9b6e2d38 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy
@@ -16,13 +16,11 @@
 
 package nextflow.cloud.google.batch.client
 
-
 import com.google.auth.oauth2.GoogleCredentials
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.Session
 import nextflow.cloud.google.GoogleOpts
-import nextflow.exception.ProcessUnrecoverableException
 import nextflow.util.MemoryUnit
 /**
  * Model Google Batch config settings
@@ -33,11 +31,14 @@ import nextflow.util.MemoryUnit
 @CompileStatic
 class BatchConfig {
 
-    static private List<Integer> DEFAULT_RETRY_LIST = List.of(50001)
+    static final private int DEFAULT_MAX_SPOT_ATTEMPTS = 0
+    
+    static final private List<Integer> DEFAULT_RETRY_LIST = List.of(50001)
 
     private GoogleOpts googleOpts
     private GoogleCredentials credentials
     private List<String> allowedLocations
+    private String bootDiskImage
     private MemoryUnit bootDiskSize
     private String cpuPlatform
     private int maxSpotAttempts
@@ -54,6 +55,7 @@ class BatchConfig {
     GoogleOpts getGoogleOpts() { return googleOpts }
     GoogleCredentials getCredentials() { return credentials }
     List<String> getAllowedLocations() { allowedLocations }
+    String getBootDiskImage() { bootDiskImage }
     MemoryUnit getBootDiskSize() { bootDiskSize }
     String getCpuPlatform() { cpuPlatform }
     int getMaxSpotAttempts() { maxSpotAttempts }
@@ -72,9 +74,10 @@ class BatchConfig {
         result.googleOpts = GoogleOpts.create(session)
         result.credentials = result.googleOpts.credentials
         result.allowedLocations = session.config.navigate('google.batch.allowedLocations', List.of()) as List<String>
+        result.bootDiskImage = session.config.navigate('google.batch.bootDiskImage')
         result.bootDiskSize = session.config.navigate('google.batch.bootDiskSize') as MemoryUnit
         result.cpuPlatform = session.config.navigate('google.batch.cpuPlatform')
-        result.maxSpotAttempts = session.config.navigate('google.batch.maxSpotAttempts',5) as int
+        result.maxSpotAttempts = session.config.navigate('google.batch.maxSpotAttempts', DEFAULT_MAX_SPOT_ATTEMPTS) as int
         result.installGpuDrivers = session.config.navigate('google.batch.installGpuDrivers',false)
         result.preemptible = session.config.navigate('google.batch.preemptible',false)
         result.spot = session.config.navigate('google.batch.spot',false)
@@ -83,7 +86,7 @@ class BatchConfig {
         result.subnetwork = session.config.navigate('google.batch.subnetwork')
         result.serviceAccountEmail = session.config.navigate('google.batch.serviceAccountEmail')
         result.retryConfig = new BatchRetryConfig( session.config.navigate('google.batch.retryPolicy') as Map ?: Map.of() )
-        result.autoRetryExitCodes = session.config.navigate('google.batch.autoRetryExitCodes',DEFAULT_RETRY_LIST) as List<Integer>
+        result.autoRetryExitCodes = session.config.navigate('google.batch.autoRetryExitCodes', DEFAULT_RETRY_LIST) as List<Integer>
         return result
     }
 
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/lifesciences/GoogleLifeSciencesExecutor.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/lifesciences/GoogleLifeSciencesExecutor.groovy
index 956b5f858e..9ef4c55894 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/lifesciences/GoogleLifeSciencesExecutor.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/lifesciences/GoogleLifeSciencesExecutor.groovy
@@ -21,6 +21,7 @@ import java.nio.file.Path
 
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
+import nextflow.SysEnv
 import nextflow.exception.AbortOperationException
 import nextflow.executor.Executor
 import nextflow.executor.SupportedScriptTypes
@@ -120,6 +121,8 @@ class GoogleLifeSciencesExecutor extends Executor implements ExtensionPoint {
 
     @Override
     protected void register() {
+        if( !SysEnv.getBool('NXF_DISABLE_GLS_DEPRECATION_NOTICE', false) )
+            log.warn "Google Cloud Life Sciences API Cloud Life Sciences is deprecated and will no longer be available on Google Cloud after July 8, 2025. Consider migrating to Google Cloud Batch instead. Read more at this link: https://cloud.google.com/life-sciences/docs/deprecations"
         super.register()
         validateWorkDir()
         createConfig()
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/lifesciences/GoogleLifeSciencesHelper.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/lifesciences/GoogleLifeSciencesHelper.groovy
index ea186ff781..8ae4bef53c 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/lifesciences/GoogleLifeSciencesHelper.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/lifesciences/GoogleLifeSciencesHelper.groovy
@@ -366,7 +366,7 @@ class GoogleLifeSciencesHelper {
         final remoteTaskDir = getRemoteTaskDir(workDir)
         def result = 'set -x; '
         result += "trap 'err=\$?; exec 1>&2; gsutil -m -q cp -R $localTaskDir/${TaskRun.CMD_LOG} ${remoteTaskDir}/${TaskRun.CMD_LOG} || true; [[ \$err -gt 0 || \$GOOGLE_LAST_EXIT_STATUS -gt 0 || \$NXF_DEBUG -gt 0 ]] && { ls -lah $localTaskDir || true; gsutil -m -q cp -R /google/ ${remoteTaskDir}; } || rm -rf $localTaskDir; exit \$err' EXIT; "
-        result += "{ cd $localTaskDir; bash ${TaskRun.CMD_RUN} nxf_unstage; } >> $localTaskDir/${TaskRun.CMD_LOG} 2>&1"
+        result += "{ cd $localTaskDir; bash ${TaskRun.CMD_RUN} nxf_unstage;} >> $localTaskDir/${TaskRun.CMD_LOG} 2>&1"
         return result
     }
 
diff --git a/plugins/nf-google/src/resources/META-INF/MANIFEST.MF b/plugins/nf-google/src/resources/META-INF/MANIFEST.MF
index 92494dcf38..fb9f7deae5 100644
--- a/plugins/nf-google/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-google/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.cloud.google.GoogleCloudPlugin
 Plugin-Id: nf-google
-Plugin-Version: 1.14.0
+Plugin-Version: 1.16.0
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=24.04.4
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy
index b54a5ff7a8..43150d17fd 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy
@@ -17,6 +17,9 @@
 
 package nextflow.cloud.google.batch
 
+import com.google.cloud.batch.v1.JobStatus
+import com.google.cloud.batch.v1.Task
+
 import java.nio.file.Path
 
 import com.google.cloud.batch.v1.GCS
@@ -105,6 +108,7 @@ class GoogleBatchTaskHandlerTest extends Specification {
         !instancePolicy.getMachineType()
         !instancePolicy.getMinCpuPlatform()
         instancePolicy.getProvisioningModel().toString() == 'PROVISIONING_MODEL_UNSPECIFIED'
+        !instancePolicy.getBootDisk().getImage()
         and:
         allocationPolicy.getLocation().getAllowedLocationsCount() == 0
         allocationPolicy.getNetwork().getNetworkInterfacesCount() == 0
@@ -121,6 +125,7 @@ class GoogleBatchTaskHandlerTest extends Specification {
         and:
         def ACCELERATOR = new AcceleratorResource(request: 1, type: 'nvidia-tesla-v100')
         def BOOT_DISK = MemoryUnit.of('10 GB')
+        def BOOT_IMAGE = 'batch-debian'
         def CONTAINER_IMAGE = 'ubuntu:22.1'
         def CONTAINER_OPTS = '--this --that'
         def CPU_PLATFORM = 'Intel Skylake'
@@ -134,6 +139,7 @@ class GoogleBatchTaskHandlerTest extends Specification {
             getConfig() >> Mock(BatchConfig) {
                 getAllowedLocations() >> ['zones/us-central1-a', 'zones/us-central1-c']
                 getBootDiskSize() >> BOOT_DISK
+                getBootDiskImage() >> BOOT_IMAGE
                 getCpuPlatform() >> CPU_PLATFORM
                 getMaxSpotAttempts() >> 5
                 getSpot() >> true
@@ -211,6 +217,7 @@ class GoogleBatchTaskHandlerTest extends Specification {
         and:
         instancePolicy.getAccelerators(0).getCount() == 1
         instancePolicy.getAccelerators(0).getType() == ACCELERATOR.type
+        instancePolicy.getBootDisk().getImage() == BOOT_IMAGE
         instancePolicy.getDisks(0).getNewDisk().getSizeGb() == DISK.request.toGiga()
         instancePolicy.getDisks(0).getNewDisk().getType() == DISK.type
         instancePolicy.getMachineType() == MACHINE_TYPE
@@ -577,4 +584,39 @@ class GoogleBatchTaskHandlerTest extends Specification {
         and:
         0 * client.deleteJob('job1') >> null
     }
+
+    JobStatus makeJobStatus(JobStatus.State state, String desc = null) {
+        final builder = JobStatus.newBuilder().setState(state)
+        if( desc ) {
+            builder.addStatusEvents(
+                StatusEvent.newBuilder()
+                    .setDescription(desc)
+            )
+        }
+        builder.build()
+    }
+
+    def 'should check job status when no tasks in job '() {
+
+        given:
+        def jobId = 'job-id'
+        def taskId = 'task-id'
+        def client = Mock(BatchClient)
+        def task = Mock(TaskRun) {
+            lazyName() >> 'foo (1)'
+        }
+        def handler = Spy(new GoogleBatchTaskHandler(jobId: jobId, taskId: taskId, client: client, task: task))
+        final message = 'Job failed when Batch tries to schedule it: Batch Error: code - CODE_MACHINE_TYPE_NOT_FOUND'
+        when:
+        client.listTasks(jobId) >>> [new LinkedList<Task>(), new LinkedList<Task>()]
+        client.getJobStatus(jobId) >>> [
+            null,
+            makeJobStatus(JobStatus.State.FAILED, 'Scheduling Failed'),
+            makeJobStatus(JobStatus.State.FAILED, message)
+        ]
+        then:
+        handler.getTaskState() == "PENDING"
+        handler.getTaskState() == "FAILED"
+        handler.getJobError().message == message
+    }
 }
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/batch/client/BatchConfigTest.groovy b/plugins/nf-google/src/test/nextflow/cloud/google/batch/client/BatchConfigTest.groovy
index e364a01667..c6fc08f104 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/batch/client/BatchConfigTest.groovy
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/batch/client/BatchConfigTest.groovy
@@ -18,6 +18,7 @@
 package nextflow.cloud.google.batch.client
 
 import nextflow.Session
+import nextflow.util.MemoryUnit
 import spock.lang.Requires
 import spock.lang.Specification
 /**
@@ -29,21 +30,20 @@ class BatchConfigTest extends Specification {
     @Requires({System.getenv('GOOGLE_APPLICATION_CREDENTIALS')})
     def 'should create batch config' () {
         given:
-        def CONFIG = [google: [
-            batch: [
-                spot: true
-            ]
-        ] ]
+        def CONFIG = [:]
         def session = Mock(Session) { getConfig()>>CONFIG }
 
         when:
         def config = BatchConfig.create(session)
         then:
-        config.getSpot()
+        !config.getSpot()
         and:
         config.retryConfig.maxAttempts == 5
-        config.maxSpotAttempts == 5
+        config.maxSpotAttempts == 0
         config.autoRetryExitCodes == [50001]
+        and:
+        !config.bootDiskImage
+        !config.bootDiskSize
     }
 
     @Requires({System.getenv('GOOGLE_APPLICATION_CREDENTIALS')})
@@ -54,7 +54,9 @@ class BatchConfigTest extends Specification {
                 spot: true,
                 maxSpotAttempts: 8,
                 autoRetryExitCodes: [50001, 50003, 50005],
-                retryPolicy: [maxAttempts: 10]
+                retryPolicy: [maxAttempts: 10],
+                bootDiskImage: 'batch-foo',
+                bootDiskSize: '100GB'
             ]
         ] ]
         def session = Mock(Session) { getConfig()>>CONFIG }
@@ -67,6 +69,9 @@ class BatchConfigTest extends Specification {
         config.retryConfig.maxAttempts == 10
         config.maxSpotAttempts == 8
         config.autoRetryExitCodes == [50001, 50003, 50005]
+        and:
+        config.bootDiskImage == 'batch-foo'
+        config.bootDiskSize == MemoryUnit.of('100GB')
     }
 
 }
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesHelperTest.groovy b/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesHelperTest.groovy
index 35cda62f0b..9db824a902 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesHelperTest.groovy
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesHelperTest.groovy
@@ -548,7 +548,7 @@ class GoogleLifeSciencesHelperTest extends GoogleSpecification {
         def unstage = helper.getUnstagingScript(dir)
         then:
         unstage ==
-                'set -x; trap \'err=$?; exec 1>&2; gsutil -m -q cp -R /work/dir/.command.log gs://my-bucket/work/dir/.command.log || true; [[ $err -gt 0 || $GOOGLE_LAST_EXIT_STATUS -gt 0 || $NXF_DEBUG -gt 0 ]] && { ls -lah /work/dir || true; gsutil -m -q cp -R /google/ gs://my-bucket/work/dir; } || rm -rf /work/dir; exit $err\' EXIT; { cd /work/dir; bash .command.run nxf_unstage; } >> /work/dir/.command.log 2>&1'
+                'set -x; trap \'err=$?; exec 1>&2; gsutil -m -q cp -R /work/dir/.command.log gs://my-bucket/work/dir/.command.log || true; [[ $err -gt 0 || $GOOGLE_LAST_EXIT_STATUS -gt 0 || $NXF_DEBUG -gt 0 ]] && { ls -lah /work/dir || true; gsutil -m -q cp -R /google/ gs://my-bucket/work/dir; } || rm -rf /work/dir; exit $err\' EXIT; { cd /work/dir; bash .command.run nxf_unstage;} >> /work/dir/.command.log 2>&1'
     }
 
     @Unroll
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/bash-wrapper-gcp.txt b/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/bash-wrapper-gcp.txt
index 70a68452aa..c7382062a1 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/bash-wrapper-gcp.txt
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/bash-wrapper-gcp.txt
@@ -168,7 +168,10 @@ nxf_fs_fcp() {
 }
 
 on_exit() {
-    exit_status=${nxf_main_ret:=$?}
+    local last_err=$?
+    local exit_status=${nxf_main_ret:=0}
+    [[ ${exit_status} -eq 0 && ${nxf_unstage_ret:=0} -ne 0 ]] && exit_status=${nxf_unstage_ret:=0}
+    [[ ${exit_status} -eq 0 && ${last_err} -ne 0 ]] && exit_status=${last_err}
     printf -- $exit_status > {{folder}}/.exitcode
     set +u
     exit $exit_status
@@ -192,12 +195,23 @@ nxf_stage() {
     nxf_parallel "${downloads[@]}"
 }
 
-nxf_unstage() {
+nxf_unstage_outputs() {
+    true
+}
+
+nxf_unstage_controls() {
     true
     gsutil -m -q cp -R .command.out gs://bucket/work/dir/.command.out || true
     gsutil -m -q cp -R .command.err gs://bucket/work/dir/.command.err || true
     gsutil -m -q cp -R .exitcode gs://bucket/work/dir/.exitcode || true
-    [[ ${nxf_main_ret:=0} != 0 ]] && return
+}
+
+nxf_unstage() {
+    if [[ ${nxf_main_ret:=0} == 0 ]]; then
+        (set -e -o pipefail; (nxf_unstage_outputs | tee -a .command.out) 3>&1 1>&2 2>&3 | tee -a .command.err)
+        nxf_unstage_ret=$?
+    fi
+    nxf_unstage_controls
 }
 
 nxf_main() {
diff --git a/plugins/nf-tower/build.gradle b/plugins/nf-tower/build.gradle
index ca7dae0a27..347d127762 100644
--- a/plugins/nf-tower/build.gradle
+++ b/plugins/nf-tower/build.gradle
@@ -37,6 +37,6 @@ dependencies {
     api "com.fasterxml.jackson.core:jackson-databind:2.12.7.1"
 
     testImplementation(testFixtures(project(":nextflow")))
-    testImplementation "org.apache.groovy:groovy:4.0.22"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.22"
+    testImplementation "org.apache.groovy:groovy:4.0.24"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.24"
 }
diff --git a/plugins/nf-tower/changelog.txt b/plugins/nf-tower/changelog.txt
index 776e4828d1..bcc8d343cf 100644
--- a/plugins/nf-tower/changelog.txt
+++ b/plugins/nf-tower/changelog.txt
@@ -1,5 +1,8 @@
 nf-tower changelog
 ===================
+1.9.3 - 27 Oct 2024
+- Fix nf-tower plugin to upload logs when early failures  (#5434) [4222442a]
+
 1.9.2 - 5 Aug 2024
 - Bump pf4j to version 3.12.0 [96117b9a]
 
diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/LogsCheckpoint.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/LogsCheckpoint.groovy
index 514a0c0c48..11aa44d786 100644
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/LogsCheckpoint.groovy
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/LogsCheckpoint.groovy
@@ -21,7 +21,9 @@ import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.Session
 import nextflow.SysEnv
+import nextflow.processor.TaskHandler
 import nextflow.trace.TraceObserver
+import nextflow.trace.TraceRecord
 import nextflow.util.Duration
 import nextflow.util.Threads
 /**
@@ -47,6 +49,7 @@ class LogsCheckpoint implements TraceObserver {
         this.config = session.config
         this.handler = new LogsHandler(session, SysEnv.get())
         this.interval = config.navigate('tower.logs.checkpoint.interval', defaultInterval()) as Duration
+        thread = Threads.start('tower-logs-checkpoint', this.&run)
     }
 
     private String defaultInterval() {
@@ -54,12 +57,12 @@ class LogsCheckpoint implements TraceObserver {
     }
 
     @Override
-    void onFlowBegin() {
-        thread = Threads.start('tower-logs-checkpoint', this.&run)
+    void onFlowComplete() {
+        this.terminated = true
+        thread.join()
     }
-
     @Override
-    void onFlowComplete() {
+    void onFlowError(TaskHandler handler, TraceRecord trace){
         this.terminated = true
         thread.join()
     }
diff --git a/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF b/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF
index ec179c25c6..9b912922bf 100644
--- a/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: io.seqera.tower.plugin.TowerPlugin
 Plugin-Id: nf-tower
-Plugin-Version: 1.9.2
+Plugin-Version: 1.9.3
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=24.04.4
diff --git a/plugins/nf-wave/build.gradle b/plugins/nf-wave/build.gradle
index ec6d173fe4..7f4f40d744 100644
--- a/plugins/nf-wave/build.gradle
+++ b/plugins/nf-wave/build.gradle
@@ -36,10 +36,10 @@ dependencies {
     api 'org.apache.commons:commons-lang3:3.12.0'
     api 'com.google.code.gson:gson:2.10.1'
     api 'org.yaml:snakeyaml:2.2'
-    api 'io.seqera:wave-api:0.11.1'
-    api 'io.seqera:wave-utils:0.12.1'
+    api 'io.seqera:wave-api:0.14.0'
+    api 'io.seqera:wave-utils:0.15.0'
 
     testImplementation(testFixtures(project(":nextflow")))
-    testImplementation "org.apache.groovy:groovy:4.0.22"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.22"
+    testImplementation "org.apache.groovy:groovy:4.0.24"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.24"
 }
diff --git a/plugins/nf-wave/changelog.txt b/plugins/nf-wave/changelog.txt
index 57b257b5ef..1a13763b31 100644
--- a/plugins/nf-wave/changelog.txt
+++ b/plugins/nf-wave/changelog.txt
@@ -1,5 +1,30 @@
 nf-wave changelog
 ==================
+1.8.0 - 3 Dec 2024
+- Fix missing wave response (#5547) [ci fast] [ee252173]
+- Update wave deps [09ccd295]
+- Fix isContainerReady when wave is disabled (#5509) [ci fast] [3215afa8]
+- Bump groovy 4.0.24 [dd71ad31]
+
+1.7.2 - 27 Oct 2024
+- Add wave mirror vs module bundles conflicts warning [b37a8a5b]
+
+1.7.1 - 14 Oct 2024
+- Change to scan.levels to scan.allowedLevels (#5401) [88a1b1b5]
+- Fix inspect concretize option [0ee29a87]
+
+1.7.0 - 13 Oct 2024
+- Add support for Wave  container status API  (#5384) [873703ad] [9ed18a88]
+- Remove unused reportsOpts (#5379) [e794e868]
+- Sunsetting Spack support in Wave [3a54cb3b]
+
+1.6.0 - 2 Oct 2024
+- Improve Wave build timeout handling (#5304) [05bef7e4]
+- Bump groovy 4.0.23 (#5303) [ci fast] [fe3e3ac7]
+
+1.5.1 - 4 Sep 2024
+- Wave client logs improvement [5a37e617]
+
 1.5.0 - 5 Aug 2024
 - Await build completion for all Wave containers [2b8117e9]
 - Bump pf4j to version 3.12.0 [96117b9a]
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/ContainerConfig.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/ContainerConfig.groovy
index 926d7f7835..2823c5c060 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/ContainerConfig.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/ContainerConfig.groovy
@@ -29,7 +29,7 @@ import nextflow.util.CacheHelper
  */
 @Canonical
 @CompileStatic
-@ToString(includePackage = false, includeNames = true)
+@ToString(includePackage = false, includeNames = true, ignoreNulls = true)
 class ContainerConfig {
 
     List<String> entrypoint
@@ -108,4 +108,16 @@ class ContainerConfig {
         }
         return CacheHelper.hasher(allMeta).hash().toString()
     }
+
+    boolean asBoolean() {
+        return !empty()
+    }
+
+    boolean empty() {
+        return !entrypoint &&
+            !cmd &&
+            !env &&
+            !workingDir &&
+            !layers
+    }
 }
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenRequest.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenRequest.groovy
index 86a9606b55..90e86df645 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenRequest.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenRequest.groovy
@@ -21,7 +21,10 @@ package io.seqera.wave.plugin
 import groovy.transform.CompileStatic
 import groovy.transform.EqualsAndHashCode
 import groovy.transform.ToString
+import io.seqera.wave.api.ImageNameStrategy
 import io.seqera.wave.api.PackagesSpec
+import io.seqera.wave.api.ScanLevel
+import io.seqera.wave.api.ScanMode
 
 /**
  * Model a request for an augmented container
@@ -135,4 +138,26 @@ class SubmitContainerTokenRequest {
      */
     PackagesSpec packages
 
+    /**
+     * The strategy applied to name a container build by wave when using
+     * the freeze option.
+     */
+    ImageNameStrategy nameStrategy;
+
+    /**
+     * Whenever use container "mirror" mode
+     */
+    boolean mirror;
+
+    /**
+     * The request security scan mode
+     */
+    ScanMode scanMode;
+
+    /**
+     * Define the allows security vulnerabilities in the container request.
+     * Empty or null means no vulnerabilities are allowed.
+     */
+    List<ScanLevel> scanLevels
+
 }
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenResponse.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenResponse.groovy
index 5c2bb110fe..2cf5e97f2c 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenResponse.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenResponse.groovy
@@ -20,7 +20,6 @@ package io.seqera.wave.plugin
 import groovy.transform.CompileStatic
 import groovy.transform.EqualsAndHashCode
 import groovy.transform.ToString
-
 /**
  * Model a response for an augmented container
  *
@@ -30,6 +29,12 @@ import groovy.transform.ToString
 @ToString(includeNames = true, includePackage = false)
 @CompileStatic
 class SubmitContainerTokenResponse {
+
+    /**
+     * Unique Id for this request
+     */
+    String requestId
+
     /**
      * A unique authorization token assigned to this request
      */
@@ -60,4 +65,20 @@ class SubmitContainerTokenResponse {
      */
     Boolean freeze;
 
+    /**
+     * When the result is a mirror container. Version v1alpha2 as later.
+     */
+    Boolean mirror
+
+    /**
+     * The id of the security scan associated with this container
+     */
+    String scanId
+
+    /**
+     * Whenever the container has been provisioned successfully or not. If false
+     * the current status needs the be check via container status API
+     */
+    Boolean succeeded
+
 }
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index 4b64f509ca..c3640ce42d 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -27,7 +27,7 @@ import java.time.Duration
 import java.time.Instant
 import java.time.OffsetDateTime
 import java.time.temporal.ChronoUnit
-import java.util.concurrent.Callable
+import java.util.concurrent.ConcurrentHashMap
 import java.util.concurrent.Executors
 import java.util.concurrent.TimeUnit
 import java.util.function.Predicate
@@ -44,9 +44,12 @@ import dev.failsafe.event.ExecutionAttemptedEvent
 import dev.failsafe.function.CheckedSupplier
 import groovy.json.JsonOutput
 import groovy.json.JsonSlurper
+import groovy.transform.Canonical
 import groovy.transform.CompileStatic
 import groovy.transform.Memoized
 import io.seqera.wave.api.BuildStatusResponse
+import io.seqera.wave.api.ContainerStatus
+import io.seqera.wave.api.ContainerStatusResponse
 import io.seqera.wave.api.PackagesSpec
 import io.seqera.wave.plugin.config.TowerConfig
 import io.seqera.wave.plugin.config.WaveConfig
@@ -57,6 +60,7 @@ import nextflow.Session
 import nextflow.SysEnv
 import nextflow.container.inspect.ContainerInspectMode
 import nextflow.container.resolver.ContainerInfo
+import nextflow.exception.ProcessUnrecoverableException
 import nextflow.fusion.FusionConfig
 import nextflow.processor.Architecture
 import nextflow.processor.TaskRun
@@ -73,6 +77,13 @@ import org.slf4j.LoggerFactory
 @CompileStatic
 class WaveClient {
 
+    @Canonical
+    static class Handle {
+        final SubmitContainerTokenResponse response
+        final Instant createdAt
+        int iteration
+    }
+
     final static public String DEFAULT_S5CMD_AMD64_URL = 'https://nf-xpack.seqera.io/s5cmd/linux_amd64_2.2.2.json'
     final static public String DEFAULT_S5CMD_ARM64_URL = 'https://nf-xpack.seqera.io/s5cmd/linux_arm64_2.2.2.json'
 
@@ -80,8 +91,6 @@ class WaveClient {
 
     public static final List<String> DEFAULT_CONDA_CHANNELS = ['conda-forge','bioconda']
 
-    private static final String DEFAULT_SPACK_ARCH = 'x86_64'
-
     private static final String DEFAULT_DOCKER_PLATFORM = 'linux/amd64'
 
     final private HttpClient httpClient
@@ -98,6 +107,8 @@ class WaveClient {
 
     private Cache<String, SubmitContainerTokenResponse> cache
 
+    private Map<String,Handle> responses = new ConcurrentHashMap<>()
+
     private Session session
 
     private volatile String accessToken
@@ -127,7 +138,7 @@ class WaveClient {
         this.packer = new Packer().withPreserveTimestamp(config.preserveFileTimestamp())
         this.waveRegistry = new URI(endpoint).getAuthority()
         // create cache
-        cache = CacheBuilder<String, SubmitContainerTokenResponse>
+        this.cache = CacheBuilder<String, Handle>
             .newBuilder()
             .expireAfterWrite(config.tokensCacheMaxDuration().toSeconds(), TimeUnit.SECONDS)
             .build()
@@ -137,6 +148,9 @@ class WaveClient {
         this.httpClient = newHttpClient()
     }
 
+    /* only for testing */
+    protected WaveClient() { }
+
     protected HttpClient newHttpClient() {
         final builder = HttpClient.newBuilder()
                 .version(HttpClient.Version.HTTP_1_1)
@@ -160,7 +174,7 @@ class WaveClient {
     }
 
     SubmitContainerTokenRequest makeRequest(WaveAssets assets) {
-        final containerConfig = assets.containerConfig ?: new ContainerConfig()
+        ContainerConfig containerConfig = assets.containerConfig ?: new ContainerConfig()
         // prepend the bundle layer
         if( assets.moduleResources!=null && assets.moduleResources.hasEntries() ) {
             containerConfig.prependLayer(makeLayer(assets.moduleResources))
@@ -181,7 +195,21 @@ class WaveClient {
 
         if( assets.containerFile && assets.packagesSpec )
             throw new IllegalArgumentException("Wave containerFile file and packages spec cannot be specified in the same request")
-        
+
+        if( config.mirrorMode() && config.freezeMode() )
+            throw new IllegalArgumentException("Wave configuration setting 'wave.mirror' and 'wave.freeze' conflicts each other")
+
+        if( config.mirrorMode() && !config.buildRepository() )
+            throw new IllegalArgumentException("Wave configuration setting 'wave.mirror' requires the use of 'wave.build.repository' to define the target registry")
+
+        if( config.mirrorMode() && !assets.containerImage )
+            throw new IllegalArgumentException("Invalid container mirror operation - missing source container")
+
+        if( config.mirrorMode() && containerConfig ) {
+            log.warn1("Wave configuration setting 'wave.mirror' conflicts with the use of module bundles - ignoring custom config for container: $assets.containerImage")
+            containerConfig = null
+        }
+
         return new SubmitContainerTokenRequest(
                 containerImage: assets.containerImage,
                 containerPlatform: assets.containerPlatform,
@@ -194,7 +222,10 @@ class WaveClient {
                 fingerprint: assets.fingerprint(),
                 freeze: config.freezeMode(),
                 format: assets.singularity ? 'sif' : null,
-                dryRun: ContainerInspectMode.active()
+                dryRun: ContainerInspectMode.active(),
+                mirror: config.mirrorMode(),
+                scanMode: config.scanMode(),
+                scanLevels: config.scanAllowedLevels()
         )
     }
 
@@ -219,6 +250,9 @@ class WaveClient {
                 workflowId: tower.workflowId,
                 freeze: config.freezeMode(),
                 dryRun: ContainerInspectMode.active(),
+                mirror: config.mirrorMode(),
+                scanMode: config.scanMode(),
+                scanLevels: config.scanAllowedLevels()
         )
         return sendRequest(request)
     }
@@ -265,13 +299,30 @@ class WaveClient {
                     throw new UnauthorizedException("Unauthorized [401] - Verify you have provided a valid access token")
             }
             else
-                throw new BadResponseException("Wave invalid response: [${resp.statusCode()}] ${resp.body()}")
+                throw new BadResponseException("Wave invalid response: POST ${uri} [${resp.statusCode()}] ${resp.body()}")
         }
         catch (IOException e) {
             throw new IllegalStateException("Unable to connect Wave service: $endpoint")
         }
     }
 
+    protected ContainerStatusResponse jsonToContainerStatusResponse(String body) {
+        final obj = new JsonSlurper().parseText(body) as Map
+        return new ContainerStatusResponse(
+            obj.id as String,
+            obj.status as ContainerStatus,
+            obj.buildId as String,
+            obj.mirrorId as String,
+            obj.scanId as String,
+            obj.vulnerabilities as Map<String,Integer>,
+            obj.succeeded as Boolean,
+            obj.reason as String,
+            obj.detailsUri as String,
+            Instant.parse(obj.creationTime as String),
+            null
+        )
+    }
+
     protected BuildStatusResponse jsonToBuildStatusResponse(String body) {
         final obj = new JsonSlurper().parseText(body) as Map
         new BuildStatusResponse(
@@ -350,12 +401,6 @@ class WaveClient {
         if( attrs.container && attrs.conda ) {
             throw new IllegalArgumentException("Process '${name}' declares both 'container' and 'conda' directives that conflict each other")
         }
-        if( attrs.container && attrs.spack ) {
-            throw new IllegalArgumentException("Process '${name}' declares both 'container' and 'spack' directives that conflict each other")
-        }
-        if( attrs.spack && attrs.conda ) {
-            throw new IllegalArgumentException("Process '${name}' declares both 'spack' and 'conda' directives that conflict each other")
-        }
         checkConflicts0(attrs, name, 'dockerfile')
         checkConflicts0(attrs, name, 'singularityfile')
     }
@@ -367,9 +412,6 @@ class WaveClient {
         if( attrs.container && attrs.get(fileType) ) {
             throw new IllegalArgumentException("Process '${name}' declares both a 'container' directive and a module bundle $fileType that conflict each other")
         }
-        if( attrs.get(fileType) && attrs.spack ) {
-            throw new IllegalArgumentException("Process '${name}' declares both a 'spack' directive and a module bundle $fileType that conflict each other")
-        }
     }
 
     Map<String,String> resolveConflicts(Map<String,String> attrs, List<String> strategy) {
@@ -411,15 +453,13 @@ class WaveClient {
     WaveAssets resolveAssets(TaskRun task, String containerImage, boolean singularity) {
         // get the bundle
         final bundle = task.getModuleBundle()
-        // get the Spack architecture
+        // get the architecture
         final arch = task.config.getArchitecture()
-        final spackArch = arch ? arch.spackArch : DEFAULT_SPACK_ARCH
         final dockerArch = arch? arch.dockerArch : DEFAULT_DOCKER_PLATFORM
         // compose the request attributes
         def attrs = new HashMap<String,String>()
         attrs.container = containerImage
         attrs.conda = task.config.conda as String
-        attrs.spack = task.config.spack as String
         if( bundle!=null && bundle.dockerfile ) {
             attrs.dockerfile = bundle.dockerfile.text
         }
@@ -435,10 +475,10 @@ class WaveClient {
             checkConflicts(attrs, task.lazyName())
 
         //  resolve the wave assets
-        return resolveAssets0(attrs, bundle, singularity, dockerArch, spackArch)
+        return resolveAssets0(attrs, bundle, singularity, dockerArch)
     }
 
-    protected WaveAssets resolveAssets0(Map<String,String> attrs, ResourcesBundle bundle, boolean singularity, String dockerArch, String spackArch) {
+    protected WaveAssets resolveAssets0(Map<String,String> attrs, ResourcesBundle bundle, boolean singularity, String dockerArch) {
 
         final scriptType = singularity ? 'singularityfile' : 'dockerfile'
         String containerScript = attrs.get(scriptType)
@@ -483,33 +523,6 @@ class WaveClient {
             }
         }
 
-        /*
-         * If 'spack' directive is specified use it to create a container file
-         * to assemble the target container
-         */
-        if( attrs.spack ) {
-            if( containerScript )
-                throw new IllegalArgumentException("Unexpected spack and dockerfile conflict while resolving wave container")
-
-            if( isSpackFile(attrs.spack) ) {
-                // create a minimal spack file with package spec from user input
-                final spackFile = Path.of(attrs.spack)
-                final spackEnv = addPackagesToSpackYaml(spackFile.text, config.spackOpts())
-                packagesSpec = new PackagesSpec()
-                    .withType(PackagesSpec.Type.SPACK)
-                    .withSpackOpts(config.spackOpts())
-                    .withEnvironment(spackEnv.bytes.encodeBase64().toString())
-            }
-            else {
-                // create a minimal spack file with package spec from user input
-                final spackEnv = spackPackagesToSpackYaml(attrs.spack, config.spackOpts())
-                packagesSpec = new PackagesSpec()
-                    .withType(PackagesSpec.Type.SPACK)
-                    .withSpackOpts(config.spackOpts())
-                    .withEnvironment(spackEnv.bytes.encodeBase64().toString())
-            }
-        }
-
         /*
          * The process should declare at least a container image name via 'container' directive
          * or a dockerfile file to build, otherwise there's no job to be done by wave
@@ -562,28 +575,84 @@ class WaveClient {
             final key = assets.fingerprint()
             log.trace "Wave fingerprint: $key; assets: $assets"
             // get from cache or submit a new request
-            final response = cache.get(key, { sendRequest(assets) } as Callable )
-            if( response.buildId && !response.cached && !ContainerInspectMode.active() ) {
-                // await the image to be available when a new image is being built
-                awaitCompletion(response.buildId)
-            }
-            // assemble the container info response
-            return new ContainerInfo(assets.containerImage, response.targetImage, key)
+            final resp = cache.get(key, () -> {
+                final ret = sendRequest(assets);
+                responses.put(key,new Handle(ret,Instant.now()));
+                return ret
+            })
+            return new ContainerInfo(assets.containerImage, resp.targetImage, key)
         }
         catch ( UncheckedExecutionException e ) {
             throw e.cause
         }
     }
 
-    void awaitCompletion(String buildId) {
-        final long maxAwait = Duration.ofMinutes(15).toMillis();
-        final long startTime = Instant.now().toEpochMilli();
-        while( !isComplete(buildId) ) {
-            if( System.currentTimeMillis()-startTime > maxAwait ) {
-                break
-            }
-            Thread.sleep(randomRange(10,15) * 1_000)
-        }
+    protected boolean checkContainerCompletion(Handle handle) {
+        final long maxAwait = config.buildMaxDuration().toMillis()
+        final startTime = handle.createdAt.toEpochMilli()
+        final containerImage = handle.response.targetImage
+        final requestId = handle.response.requestId
+        final resp = containerStatus(requestId)
+        if( resp.status==ContainerStatus.DONE ) {
+            if( resp.succeeded )
+                return true
+            def msg = "Wave provisioning for container '${containerImage}' did not complete successfully"
+            if( resp.reason )
+                msg += "\n- Reason: ${resp.reason}"
+            if( resp.detailsUri )
+                msg += "\n- Find out more here: ${resp.detailsUri}"
+            throw new ProcessUnrecoverableException(msg)
+        }
+        if( System.currentTimeMillis()-startTime > maxAwait ) {
+            final msg = "Wave provisioning for container '${containerImage}' is exceeding max allowed duration (${config.buildMaxDuration()}) - check details here: ${endpoint}/view/containers/${requestId}"
+            throw new ProcessUnrecoverableException(msg)
+        }
+        // this is expected to be invoked ~ every seconds, therefore
+        // print an info message after 10 seconds or every 200 seconds
+        if( ((handle.iteration++)-10) % 200 == 0 ) {
+            log.info "Awaiting container provisioning: $containerImage"
+        }
+        return false
+    }
+
+    protected boolean checkBuildCompletion(Handle handle) {
+        final long maxAwait = config.buildMaxDuration().toMillis()
+        final startTime = handle.createdAt.toEpochMilli()
+        final containerImage = handle.response.targetImage
+        final buildId = handle.response.buildId
+        final resp = buildStatus(buildId)
+        if( resp.status==BuildStatusResponse.Status.COMPLETED ) {
+            if( resp.succeeded )
+                return true
+            final msg = "Wave provisioning for container '${containerImage}' did not complete successfully - check details here: ${endpoint}/view/builds/${buildId}"
+            throw new ProcessUnrecoverableException(msg)
+        }
+        if( System.currentTimeMillis()-startTime > maxAwait ) {
+            final msg = "Wave provisioning for container '${containerImage}' is exceeding max allowed duration (${config.buildMaxDuration()}) - check details here: ${endpoint}/view/builds/${buildId}"
+            throw new ProcessUnrecoverableException(msg)
+        }
+        // this is expected to be invoked ~ every seconds, therefore
+        // print an info message after 10 seconds or every 200 seconds
+        if( ((handle.iteration++)-10) % 200 == 0 ) {
+            log.info "Awaiting container provisioning: $containerImage"
+        }
+        return false
+    }
+
+    boolean isContainerReady(String key) {
+        final handle = responses.get(key)
+        if( !handle )
+            throw new IllegalStateException("Unable to find any container with key: $key")
+        final resp = handle.response
+        if( resp.requestId ) {
+            return resp.succeeded
+                    ? true
+                    : checkContainerCompletion(handle)
+        }
+        if( resp.buildId && !resp.cached )
+            return checkBuildCompletion(handle)
+        else
+            return true
     }
 
     protected static int randomRange(int min, int max) {
@@ -592,8 +661,28 @@ class WaveClient {
         return rand.nextInt((max - min) + 1) + min;
     }
 
-    protected boolean isComplete(String buildId) {
-        final String statusEndpoint = endpoint + "/v1alpha1/builds/"+buildId+"/status";
+    protected ContainerStatusResponse containerStatus(String requestId) {
+        final String statusEndpoint = endpoint + "/v1alpha2/container/${requestId}/status";
+        final HttpRequest req = HttpRequest.newBuilder()
+            .uri(URI.create(statusEndpoint))
+            .headers("Content-Type","application/json")
+            .GET()
+            .build();
+
+        final HttpResponse<String> resp = httpSend(req);
+        log.debug("Wave container status response: statusCode={}; body={}", resp.statusCode(), resp.body())
+        if( resp.statusCode()==200 ) {
+            return jsonToContainerStatusResponse(resp.body())
+        }
+        else {
+            String msg = String.format("Wave invalid response: GET %s [%s] %s", statusEndpoint, resp.statusCode(), resp.body());
+            throw new BadResponseException(msg)
+        }
+    }
+
+    @Deprecated
+    protected BuildStatusResponse buildStatus(String buildId) {
+        final String statusEndpoint = endpoint + "/v1alpha1/builds/${buildId}/status";
         final HttpRequest req = HttpRequest.newBuilder()
             .uri(URI.create(statusEndpoint))
             .headers("Content-Type","application/json")
@@ -603,8 +692,7 @@ class WaveClient {
         final HttpResponse<String> resp = httpSend(req);
         log.debug("Wave build status response: statusCode={}; body={}", resp.statusCode(), resp.body())
         if( resp.statusCode()==200 ) {
-            final result = jsonToBuildStatusResponse(resp.body())
-            return result.status == BuildStatusResponse.Status.COMPLETED
+            return jsonToBuildStatusResponse(resp.body())
         }
         else {
             String msg = String.format("Wave invalid response: GET %s [%s] %s", statusEndpoint, resp.statusCode(), resp.body());
@@ -626,12 +714,6 @@ class WaveClient {
         value.startsWith('http://') || value.startsWith('https://')
     }
 
-    protected boolean isSpackFile(String value) {
-        if( value.contains('\n') )
-            return false
-        return value.endsWith('.yaml') || value.endsWith('.yml')
-    }
-
     protected boolean refreshJwtToken0(String refresh) {
         log.debug "Token refresh request >> $refresh"
 
@@ -684,7 +766,7 @@ class WaveClient {
         final cfg = config.retryOpts()
         final listener = new EventListener<ExecutionAttemptedEvent<T>>() {
             @Override
-            void accept(ExecutionAttemptedEvent<T> event) throws Throwable {
+            void accept(ExecutionAttemptedEvent event) throws Throwable {
                 def msg = "Wave connection failure - attempt: ${event.attemptCount}"
                 if( event.lastResult!=null )
                     msg += "; response: ${event.lastResult}"
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy
index 09c5afadaf..af40573172 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy
@@ -20,6 +20,8 @@ package io.seqera.wave.plugin.config
 import groovy.transform.CompileStatic
 import groovy.transform.ToString
 import groovy.util.logging.Slf4j
+import io.seqera.wave.api.ScanLevel
+import io.seqera.wave.api.ScanMode
 import io.seqera.wave.config.CondaOpts
 import io.seqera.wave.config.SpackOpts
 import nextflow.file.FileHelper
@@ -30,7 +32,7 @@ import nextflow.util.Duration
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
 @Slf4j
-@ToString(includeNames = true, includePackage = false, includeFields = true, excludes = 'reportOpts')
+@ToString(includeNames = true, includePackage = false, includeFields = true)
 @CompileStatic
 class WaveConfig {
     final private static String DEF_ENDPOINT = 'https://wave.seqera.io'
@@ -45,16 +47,20 @@ class WaveConfig {
     final private Boolean bundleProjectResources
     final private String buildRepository
     final private String cacheRepository
-    final private ReportOpts reportOpts
     final private RetryOpts retryOpts
     final private HttpOpts httpClientOpts
     final private Boolean freezeMode
     final private Boolean preserveFileTimestamp
+    final private Duration buildMaxDuration
+    final private Boolean mirrorMode
+    final private ScanMode scanMode
+    final private List<ScanLevel> scanAllowedLevels
 
     WaveConfig(Map opts, Map<String,String> env=System.getenv()) {
         this.enabled = opts.enabled
         this.endpoint = (opts.endpoint?.toString() ?: env.get('WAVE_API_ENDPOINT') ?: DEF_ENDPOINT)?.stripEnd('/')
-        this.freezeMode = opts.freeze as Boolean
+        this.freezeMode = opts.freeze
+        this.mirrorMode = opts.mirror
         this.preserveFileTimestamp = opts.preserveFileTimestamp as Boolean
         this.containerConfigUrl = parseConfig(opts, env)
         this.tokensCacheMaxDuration = opts.navigate('tokens.cache.maxDuration', '30m') as Duration
@@ -64,9 +70,11 @@ class WaveConfig {
         this.cacheRepository = opts.navigate('build.cacheRepository') as String
         this.strategy = parseStrategy(opts.strategy)
         this.bundleProjectResources = opts.bundleProjectResources
-        this.reportOpts = new ReportOpts(opts.report as Map ?: Map.of())
         this.retryOpts = retryOpts0(opts)
         this.httpClientOpts = new HttpOpts(opts.httpClient as Map ?: Map.of())
+        this.buildMaxDuration = opts.navigate('build.maxDuration', '40m') as Duration
+        this.scanMode = opts.navigate('scan.mode') as ScanMode
+        this.scanAllowedLevels = parseScanLevels(opts.navigate('scan.allowedLevels'))
         // some validation
         validateConfig()
     }
@@ -87,6 +95,8 @@ class WaveConfig {
 
     boolean freezeMode() { return this.freezeMode }
 
+    boolean mirrorMode() { return this.mirrorMode }
+
     boolean preserveFileTimestamp() { return this.preserveFileTimestamp }
 
     boolean bundleProjectResources() { bundleProjectResources }
@@ -95,6 +105,8 @@ class WaveConfig {
 
     String cacheRepository() { cacheRepository }
 
+    Duration buildMaxDuration() { buildMaxDuration }
+
     private void validateConfig() {
         def scheme= FileHelper.getUrlProtocol(endpoint)
         if( scheme !in ['http','https'] )
@@ -164,6 +176,24 @@ class WaveConfig {
         return tokensCacheMaxDuration 
     }
 
-    @Deprecated
-    ReportOpts reportOpts() { reportOpts }
+    ScanMode scanMode() {
+        return scanMode
+    }
+
+    List<ScanLevel> scanAllowedLevels() {
+        return scanAllowedLevels
+    }
+
+    protected List<ScanLevel> parseScanLevels(value) {
+        if( !value )
+            return null
+        if( value instanceof CharSequence ) {
+            final str = value.toString()
+            value = str.tokenize(',').collect(it->it.trim())
+        }
+        if( value instanceof List ) {
+            return (value as List).collect(it-> ScanLevel.valueOf(it.toString().toUpperCase()))
+        }
+        throw new IllegalArgumentException("Invalid value for 'wave.scan.levels' setting - offending value: $value; type: ${value.getClass().getName()}")
+    }
 }
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy
index 914d73befe..69521b9e78 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy
@@ -127,4 +127,11 @@ class WaveContainerResolver implements ContainerResolver {
         return null
     }
 
+    @Override
+    boolean isContainerReady(String key) {
+        final c=client()
+        return c.enabled()
+            ? c.isContainerReady(key)
+            : defaultResolver.isContainerReady(key)
+    }
 }
diff --git a/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF b/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
index 696026aa07..bb42c60b97 100644
--- a/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: io.seqera.wave.plugin.WavePlugin
 Plugin-Id: nf-wave
-Plugin-Version: 1.5.0
+Plugin-Version: 1.8.0
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=24.04.4
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/ContainerConfigTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/ContainerConfigTest.groovy
index ec634488f6..87e4f0c927 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/ContainerConfigTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/ContainerConfigTest.groovy
@@ -161,4 +161,20 @@ class ContainerConfigTest extends Specification {
         fusion1.fingerprint() != fusion2.fingerprint()
         config1.fingerprint() == config2.fingerprint()
     }
+
+    def 'should validate empty' () {
+        expect:
+        new ContainerConfig().empty()
+        new ContainerConfig([], null, null, null, null).empty()
+        new ContainerConfig(null, [], null, null, null).empty()
+        new ContainerConfig(null, null, [], null, null).empty()
+        new ContainerConfig(null, null, null, '', null).empty()
+        new ContainerConfig(null, null, null, null, []).empty()
+        and:
+        !new ContainerConfig(['x'], null, null, null, null).empty()
+        !new ContainerConfig(null, ['x'], null, null, null).empty()
+        !new ContainerConfig(null, null, ['x'], null, null).empty()
+        !new ContainerConfig(null, null, null, 'x', null).empty()
+        !new ContainerConfig(null, null, null, null, [new ContainerLayer()]).empty()
+    }
 }
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
index 9b7eab4781..1f54b0a3d7 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -18,7 +18,6 @@
 package io.seqera.wave.plugin
 
 import static java.nio.file.StandardOpenOption.*
-import static test.TestHelper.*
 
 import java.net.http.HttpRequest
 import java.nio.file.Files
@@ -35,11 +34,16 @@ import groovy.json.JsonOutput
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import io.seqera.wave.api.BuildStatusResponse
+import io.seqera.wave.api.ContainerStatus
+import io.seqera.wave.api.ContainerStatusResponse
 import io.seqera.wave.api.PackagesSpec
+import io.seqera.wave.api.ScanLevel
+import io.seqera.wave.api.ScanMode
 import io.seqera.wave.config.CondaOpts
 import nextflow.Session
 import nextflow.SysEnv
 import nextflow.container.inspect.ContainerInspectMode
+import nextflow.exception.ProcessUnrecoverableException
 import nextflow.extension.FilesEx
 import nextflow.file.FileHelper
 import nextflow.processor.TaskRun
@@ -48,9 +52,11 @@ import org.apache.commons.compress.archivers.ArchiveStreamFactory
 import org.apache.commons.compress.archivers.tar.TarArchiveEntry
 import org.apache.commons.compress.archivers.tar.TarArchiveInputStream
 import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream
+import org.junit.Rule
 import spock.lang.Shared
 import spock.lang.Specification
 import spock.lang.Unroll
+import test.OutputCapture
 /**
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
@@ -99,6 +105,9 @@ class WaveClientTest extends Specification {
         }
     }
 
+    @Rule
+    OutputCapture capture = new OutputCapture()
+
     def 'should tar file' () {
         given:
         def LAST_MODIFIED = FileTime.fromMillis(1_000_000_000_000)
@@ -219,6 +228,7 @@ class WaveClientTest extends Specification {
         !req.condaFile
         !req.spackFile
         !req.containerConfig.layers
+        !req.mirror
         and:
         req.freeze
         and:
@@ -226,6 +236,53 @@ class WaveClientTest extends Specification {
         req.timestamp instanceof String
     }
 
+    def 'should create request object with mirror mode' () {
+        given:
+        def session = Mock(Session) { getConfig() >> [wave:[mirror:true, build: [repository: 'quay.io']]]}
+        def IMAGE =  'foo:latest'
+        def wave = new WaveClient(session)
+
+        when:
+        def req = wave.makeRequest(WaveAssets.fromImage(IMAGE))
+        then:
+        req.containerImage == IMAGE
+        !req.containerPlatform
+        !req.containerFile
+        !req.condaFile
+        !req.spackFile
+        !req.containerConfig.layers
+        !req.freeze
+        and:
+        req.mirror
+        req.buildRepository == 'quay.io'
+        and:
+        req.fingerprint == 'bd2cb4b32df41f2d290ce2366609f2ad'
+        req.timestamp instanceof String
+    }
+
+    def 'should create request object with scan mode and levels' () {
+        given:
+        def session = Mock(Session) { getConfig() >> [wave:[scan:[mode: 'required', allowedLevels: 'low,medium']]]}
+        def IMAGE =  'foo:latest'
+        def wave = new WaveClient(session)
+
+        when:
+        def req = wave.makeRequest(WaveAssets.fromImage(IMAGE))
+        then:
+        req.containerImage == IMAGE
+        !req.containerPlatform
+        !req.containerFile
+        !req.condaFile
+        !req.spackFile
+        !req.containerConfig.layers
+        and:
+        req.scanMode == ScanMode.required
+        req.scanLevels == List.of(ScanLevel.LOW, ScanLevel.MEDIUM)
+        and:
+        req.fingerprint == 'bd2cb4b32df41f2d290ce2366609f2ad'
+        req.timestamp instanceof String
+    }
+
     def 'should create request object with dry-run mode' () {
         given:
         ContainerInspectMode.activate(true)
@@ -565,33 +622,6 @@ class WaveClientTest extends Specification {
         assets.packagesSpec.channels == WaveClient.DEFAULT_CONDA_CHANNELS
     }
 
-    def 'should create asset with spack recipe' () {
-        given:
-        def session = Mock(Session) { getConfig() >> [:]}
-        and:
-        def task = Mock(TaskRun) {getConfig() >> [spack:"rseqc@3.0.1 'rbase@3.5'", arch:"amd64"] }
-        and:
-        def client = new WaveClient(session)
-
-        when:
-        def assets = client.resolveAssets(task, null, false)
-        then:
-        !assets.containerFile
-        !assets.moduleResources
-        !assets.containerImage
-        !assets.containerConfig
-        !assets.projectResources
-        and:
-        assets.packagesSpec.type == PackagesSpec.Type.SPACK
-        assets.packagesSpec.entries == null
-        and:
-        new String(assets.packagesSpec.environment.decodeBase64()) == '''\
-                spack:
-                  specs: [rseqc@3.0.1, rbase@3.5]
-                  concretizer: {unify: true, reuse: false}
-                '''.stripIndent(true)
-    }
-
     def 'should create asset with conda file' () {
         given:
         def folder = Files.createTempDirectory('test')
@@ -619,32 +649,6 @@ class WaveClientTest extends Specification {
         folder?.deleteDir()
     }
 
-    def 'should create asset with spack file' () {
-        given:
-        def folder = Files.createTempDirectory('test')
-        def spackFile = folder.resolve('spack.yaml'); spackFile.text = 'the-spack-recipe-here'
-        and:
-        def session = Mock(Session) { getConfig() >> [:]}
-        def task = Mock(TaskRun) {getConfig() >> [spack:spackFile.toString(), arch: 'amd64'] }
-        and:
-        def client = new WaveClient(session)
-
-        when:
-        def assets = client.resolveAssets(task, null, false)
-        then:
-        !assets.containerFile
-        !assets.moduleResources
-        !assets.containerImage
-        !assets.containerConfig
-        !assets.projectResources
-        and:
-        assets.packagesSpec.type == PackagesSpec.Type.SPACK
-        new String(assets.packagesSpec.environment.decodeBase64()) == 'the-spack-recipe-here'
-        !assets.packagesSpec.entries
-
-        cleanup:
-        folder?.deleteDir()
-    }
 
     // ==== singularity native build + conda ====
 
@@ -723,70 +727,6 @@ class WaveClientTest extends Specification {
         folder?.deleteDir()
     }
 
-    def 'should create assets with spack recipe for singularity' () {
-        given:
-        def session = Mock(Session) { getConfig() >> [wave:[build:[spack:[commands: ['cmd-foo','cmd-bar']]]]]}
-        and:
-        def task = Mock(TaskRun) {getConfig() >> [spack:"rseqc@3.0.1 'rbase@3.5'", arch:"amd64"] }
-        and:
-        def client = new WaveClient(session)
-
-        when:
-        def assets = client.resolveAssets(task, null, true)
-        then:
-        !assets.containerFile
-        !assets.moduleResources
-        !assets.containerImage
-        !assets.containerConfig
-        !assets.projectResources
-        and:
-        assets.packagesSpec.type == PackagesSpec.Type.SPACK
-        assets.packagesSpec.entries == null
-        assets.packagesSpec.spackOpts.commands == ['cmd-foo','cmd-bar']
-        decodeBase64(assets.packagesSpec.environment) == '''\
-                spack:
-                  specs: [rseqc@3.0.1, rbase@3.5]
-                  concretizer: {unify: true, reuse: false}
-                '''.stripIndent(true)
-    }
-
-    def 'should create asset with spack file for singularity' () {
-        given:
-        def folder = Files.createTempDirectory('test')
-        def spackFile = folder.resolve('spack.yml');
-        spackFile.text = '''\
-                spack:
-                  specs: [rseqc@3.0.1, rbase@3.5]
-                  concretizer: {unify: true, reuse: false}
-                '''.stripIndent(true)
-        and:
-        def session = Mock(Session) { getConfig() >> [wave:[build:[spack:[basePackages: 'nano@1.2.3']]]]}
-        def task = Mock(TaskRun) {getConfig() >> [spack:spackFile.toString()] }
-        and:
-        def client = new WaveClient(session)
-
-        when:
-        def assets = client.resolveAssets(task, null, true)
-        then:
-        assets.singularity
-        and:
-        !assets.containerFile
-        !assets.moduleResources
-        !assets.containerImage
-        !assets.containerConfig
-        !assets.projectResources
-        and:
-        assets.packagesSpec.type == PackagesSpec.Type.SPACK
-        assets.packagesSpec.spackOpts.basePackages == 'nano@1.2.3'
-        decodeBase64(assets.packagesSpec.environment) == '''\
-                spack:
-                  specs: [rseqc@3.0.1, rbase@3.5, nano@1.2.3]
-                  concretizer: {unify: true, reuse: false}
-                '''.stripIndent(true)
-
-        cleanup:
-        folder?.deleteDir()
-    }
 
     def 'should create assets with project resources' () {
         given:
@@ -895,24 +835,6 @@ class WaveClientTest extends Specification {
         e = thrown(IllegalArgumentException)
         e.message == "Process 'foo' declares both a 'container' directive and a module bundle dockerfile that conflict each other"
 
-        when:
-        client.checkConflicts([spack:'this', dockerfile:'that'], 'foo')
-        then:
-        e = thrown(IllegalArgumentException)
-        e.message == "Process 'foo' declares both a 'spack' directive and a module bundle dockerfile that conflict each other"
-
-        when:
-        client.checkConflicts([spack:'this', container:'that'], 'foo')
-        then:
-        e = thrown(IllegalArgumentException)
-        e.message == "Process 'foo' declares both 'container' and 'spack' directives that conflict each other"
-
-        when:
-        client.checkConflicts([conda:'this', spack:'that'], 'foo')
-        then:
-        e = thrown(IllegalArgumentException)
-        e.message == "Process 'foo' declares both 'spack' and 'conda' directives that conflict each other"
-
         // singularity file checks
         when:
         client.checkConflicts([conda:'this', singularityfile:'that'], 'foo')
@@ -926,12 +848,6 @@ class WaveClientTest extends Specification {
         e = thrown(IllegalArgumentException)
         e.message == "Process 'foo' declares both a 'container' directive and a module bundle singularityfile that conflict each other"
 
-        when:
-        client.checkConflicts([spack:'this', singularityfile:'that'], 'foo')
-        then:
-        e = thrown(IllegalArgumentException)
-        e.message == "Process 'foo' declares both a 'spack' directive and a module bundle singularityfile that conflict each other"
-
     }
 
     def 'should get project resource bundle' () {
@@ -1178,27 +1094,53 @@ class WaveClientTest extends Specification {
 
     def 'should deserialize build status' () {
         given:
+        def timestamp = Instant.parse('2024-10-07T20:41:00.804699Z')
         def sess = Mock(Session) {getConfig() >> [:] }
         and:
         def wave = Spy(new WaveClient(sess))
         and:
-        def b1 = '{"id":"3449a9d02831c406_1","status":"PENDING","startTime":"2024-04-11T20:42:56.917524490Z"}'
-        def b2 = '{"id":"f76b765d2a9cec8b_1","status":"COMPLETED","startTime":"2024-04-11T21:46:55.960337916Z","duration":51.092386813,"succeeded":true}'
+        def json = '''
+            {
+               "id":"1234",
+               "buildId":"bd-12345",
+               "creationTime":"2024-10-07T20:41:00.804699Z",
+               "detailsUri":"http://foo.com/view/123",
+               "duration":"60000000000",
+               "mirrorId":"mr-12345",
+               "reason":"Some err message",
+               "scanId":"sc-12345",
+               "status":"DONE",
+               "succeeded":true,
+               "vulnerabilities":{
+                  "LOW":1,
+                  "MEDIUM":2
+               }
+            }
+            '''.stripIndent()
 
-        expect:
-        wave.jsonToBuildStatusResponse(b1) == new BuildStatusResponse(
-            '3449a9d02831c406_1',
-            BuildStatusResponse.Status.PENDING,
-            Instant.parse("2024-04-11T20:42:56.917524490Z"),
+        when:
+        def resp = wave.jsonToContainerStatusResponse(json)
+        then:
+        resp == new ContainerStatusResponse(
+            '1234',
+            ContainerStatus.DONE,
+            'bd-12345',
+            'mr-12345',
+            'sc-12345',
+            [LOW: 1, MEDIUM: 2],
+            true,
+            'Some err message',
+            'http://foo.com/view/123',
+            timestamp,
             null,
-            null)
-        and:
-        wave.jsonToBuildStatusResponse(b2) == new BuildStatusResponse(
-            'f76b765d2a9cec8b_1',
-            BuildStatusResponse.Status.COMPLETED,
-            Instant.parse("2024-04-11T21:46:55.960337916Z"),
-            Duration.ofMillis(51.092386813 * 1_000 as long),
-            true)
+        )
+    }
+
+    def 'should deserialize container status' () {
+        given:
+        def sess = Mock(Session) {getConfig() >> [:] }
+        and:
+        def wave = Spy(new WaveClient(sess))
     }
 
     def 'should test range' () {
@@ -1209,4 +1151,249 @@ class WaveClientTest extends Specification {
         100 .times { assert WaveClient.randomRange(0, 10) >= 0 }
     }
 
+    def 'should report true on build completion' () {
+        given:
+        def sess = Mock(Session) {getConfig() >> [:] }
+        and:
+        def wave = Spy(new WaveClient(sess))
+        def BUILD_ID = 'build-123'
+        def PENDING = new BuildStatusResponse('123', BuildStatusResponse.Status.PENDING, Instant.now(), null, null)
+        def COMPLETED = new BuildStatusResponse('123', BuildStatusResponse.Status.COMPLETED, Instant.now(), Duration.ofMillis(1), true)
+        and:
+        def response = new SubmitContainerTokenResponse(buildId: BUILD_ID, targetImage: 'my/container:latest')
+
+        when:
+        def done = wave.checkBuildCompletion(new WaveClient.Handle(response,Instant.now()))
+        then:
+        1 * wave.buildStatus(BUILD_ID) >> PENDING
+        and:
+        !done
+
+        when:
+        done = wave.checkBuildCompletion(new WaveClient.Handle(response,Instant.now()))
+        then:
+        1 * wave.buildStatus(BUILD_ID) >> COMPLETED
+        and:
+        done
+    }
+
+    def 'should report an exception on build failure' () {
+        given:
+        def sess = Mock(Session) {getConfig() >> [:] }
+        and:
+        def wave = Spy(new WaveClient(sess))
+        def BUILD_ID = 'build-123'
+        def PENDING = new BuildStatusResponse('123', BuildStatusResponse.Status.PENDING, Instant.now(), null, null)
+        def FAILED = new BuildStatusResponse('123', BuildStatusResponse.Status.COMPLETED, Instant.now(), Duration.ofMillis(1), false)
+        and:
+        def response = new SubmitContainerTokenResponse(buildId: BUILD_ID, targetImage: 'my/container:latest')
+
+        when:
+        def done = wave.checkBuildCompletion(new WaveClient.Handle(response,Instant.now()))
+        then:
+        1 * wave.buildStatus(BUILD_ID) >> PENDING
+        and:
+        !done
+
+        when:
+        wave.checkBuildCompletion(new WaveClient.Handle(response,Instant.now()))
+        then:
+        1 * wave.buildStatus(BUILD_ID) >> FAILED
+        and:
+        def err = thrown(ProcessUnrecoverableException)
+        err.message == "Wave provisioning for container 'my/container:latest' did not complete successfully - check details here: https://wave.seqera.io/view/builds/build-123"
+    }
+
+    def 'should fail on build timeout' () {
+        given:
+        def sess = Mock(Session) {getConfig() >> [wave: [build:[maxDuration: '500ms']]] }
+        and:
+        def wave = Spy(new WaveClient(sess))
+        def BUILD_ID = 'build-123'
+        def PENDING = new BuildStatusResponse('123', BuildStatusResponse.Status.PENDING, Instant.now(), null, null)
+        and:
+        def response = new SubmitContainerTokenResponse(buildId: BUILD_ID, targetImage: 'my/container:latest')
+
+        when:
+        wave.checkBuildCompletion(new WaveClient.Handle(response,Instant.now().minusSeconds(10)))
+        then:
+        1 * wave.buildStatus(BUILD_ID) >> PENDING
+        
+        then:
+        def err = thrown(ProcessUnrecoverableException)
+        err.message == "Wave provisioning for container 'my/container:latest' is exceeding max allowed duration (500ms) - check details here: https://wave.seqera.io/view/builds/build-123"
+    }
+
+    // == new api
+
+    def 'should report true on container completion' () {
+        given:
+        def sess = Mock(Session) {getConfig() >> [:] }
+        and:
+        def wave = Spy(new WaveClient(sess))
+        def ID = '123'
+        def PENDING = new ContainerStatusResponse('123', ContainerStatus.PENDING, 'bd-123', null, 'sc-123', [:], null, null, null, Instant.now(), null )
+        def COMPLETED = new ContainerStatusResponse('123', ContainerStatus.DONE, 'bd-123', null, 'sc-123', [:], true, null, null, Instant.now(), Duration.ofMinutes(1))
+        and:
+        def response = new SubmitContainerTokenResponse(requestId: ID, buildId: 'bd-123', targetImage: 'my/container:latest')
+
+        when:
+        def done = wave.checkContainerCompletion(new WaveClient.Handle(response,Instant.now()))
+        then:
+        1 * wave.containerStatus(ID) >> PENDING
+        and:
+        !done
+
+        when:
+        done = wave.checkContainerCompletion(new WaveClient.Handle(response,Instant.now()))
+        then:
+        1 * wave.containerStatus(ID) >> COMPLETED
+        and:
+        done
+    }
+
+    def 'should report an exception on build failure' () {
+        given:
+        def sess = Mock(Session) {getConfig() >> [:] }
+        and:
+        def wave = Spy(new WaveClient(sess))
+        def ID = '123'
+        def PENDING = new ContainerStatusResponse('123', ContainerStatus.PENDING, 'bd-123', null, 'sc-123', [:], null, null, null, Instant.now(), null )
+        def FAILED = new ContainerStatusResponse('123', ContainerStatus.DONE, 'bd-123', null, 'sc-123', [:], false, null, 'https://wave.seqera.io/view/builds/build-123', Instant.now(), Duration.ofMinutes(1))
+        and:
+        def response = new SubmitContainerTokenResponse(requestId: ID, buildId: 'bd-123', targetImage: 'my/container:latest')
+
+        when:
+        def done = wave.checkContainerCompletion(new WaveClient.Handle(response,Instant.now()))
+        then:
+        1 * wave.containerStatus(ID) >> PENDING
+        and:
+        !done
+
+        when:
+        wave.checkContainerCompletion(new WaveClient.Handle(response,Instant.now()))
+        then:
+        1 * wave.containerStatus(ID) >> FAILED
+        and:
+        def err = thrown(ProcessUnrecoverableException)
+        err.message == "Wave provisioning for container 'my/container:latest' did not complete successfully\n- Find out more here: https://wave.seqera.io/view/builds/build-123"
+    }
+
+    def 'should fail on build timeout' () {
+        given:
+        def sess = Mock(Session) {getConfig() >> [wave: [build:[maxDuration: '500ms']]] }
+        and:
+        def wave = Spy(new WaveClient(sess))
+        def ID = '123'
+        def PENDING = new ContainerStatusResponse('123', ContainerStatus.PENDING, 'bd-123', null, 'sc-123', [:], null, null, null, Instant.now(), null )
+        and:
+        def response = new SubmitContainerTokenResponse(requestId: ID, buildId: 'bd-123', targetImage: 'my/container:latest')
+
+        when:
+        wave.checkContainerCompletion(new WaveClient.Handle(response,Instant.now().minusSeconds(10)))
+        then:
+        1 * wave.containerStatus(ID) >> PENDING
+
+        then:
+        def err = thrown(ProcessUnrecoverableException)
+        err.message == "Wave provisioning for container 'my/container:latest' is exceeding max allowed duration (500ms) - check details here: https://wave.seqera.io/view/containers/123"
+    }
+
+    def 'should validate isContainerReady' () {
+        given:
+        def sess = Mock(Session) {getConfig() >> [wave: [build:[maxDuration: '500ms']]] }
+        def cache = Mock(Map)
+        and:
+        def resp = Mock(SubmitContainerTokenResponse)
+        def handle = new WaveClient.Handle(resp,Instant.now())
+        def wave = Spy(new WaveClient(session:sess, responses: cache))
+        boolean ready
+
+        // container succeeded
+        when:
+        ready = wave.isContainerReady('xyz')
+        then:
+        cache.get('xyz') >> handle
+        and:
+        resp.requestId >> '12345'
+        resp.succeeded >> true
+        and:
+        0 * wave.checkContainerCompletion(handle) >> null
+        0 * wave.checkBuildCompletion(_) >> null
+        and:
+        ready
+
+        // container is pending
+        when:
+        ready = wave.isContainerReady('xyz')
+        then:
+        cache.get('xyz') >> handle
+        and:
+        resp.requestId >> '12345'
+        resp.succeeded >> null
+        and:
+        1 * wave.checkContainerCompletion(handle) >> true
+        0 * wave.checkBuildCompletion(_) >> null
+        and:
+        ready
+
+        // container failed
+        when:
+        ready = wave.isContainerReady('xyz')
+        then:
+        cache.get('xyz') >> handle
+        and:
+        resp.requestId >> '12345'
+        resp.succeeded >> false
+        and:
+        1 * wave.checkContainerCompletion(handle) >> false
+        0 * wave.checkBuildCompletion(_) >> null
+        and:
+        !ready
+
+
+        // build is READY
+        when:
+        ready = wave.isContainerReady('xyz')
+        then:
+        cache.get('xyz') >> handle
+        and:
+        resp.buildId >> 'bd-5678'
+        resp.cached >> false
+        and:
+        0 * wave.checkContainerCompletion(_) >> null
+        1 * wave.checkBuildCompletion(handle) >> true
+        and:
+        ready
+
+        // build is not ready
+        when:
+        ready = wave.isContainerReady('xyz')
+        then:
+        cache.get('xyz') >> handle
+        and:
+        resp.requestId >> null
+        resp.buildId >> 'bd-5678'
+        resp.cached >> false
+        and:
+        0 * wave.checkContainerCompletion(_) >> null
+        1 * wave.checkBuildCompletion(handle) >> false
+        and:
+        !ready
+
+        // build is cached
+        when:
+        ready = wave.isContainerReady('xyz')
+        then:
+        cache.get('xyz') >> handle
+        and:
+        resp.requestId >> null
+        resp.buildId >> 'bd-5678'
+        resp.cached >> true
+        and:
+        0 * wave.checkContainerCompletion(_) >> null
+        0 * wave.checkBuildCompletion(handle) >> null
+        and:
+        ready
+    }
 }
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
index 613a14ee4b..fe95425528 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
@@ -17,6 +17,8 @@
 
 package io.seqera.wave.plugin.config
 
+import io.seqera.wave.api.ScanLevel
+import io.seqera.wave.api.ScanMode
 import nextflow.util.Duration
 import spock.lang.Specification
 import spock.lang.Unroll
@@ -86,7 +88,7 @@ class WaveConfigTest extends Specification {
         when:
         def opts = new WaveConfig([:])
         then:
-        opts.condaOpts().mambaImage == 'mambaorg/micromamba:1.5.8-lunar'
+        opts.condaOpts().mambaImage == 'mambaorg/micromamba:1.5.10-noble'
         opts.condaOpts().commands == null
 
         when:
@@ -199,10 +201,10 @@ class WaveConfigTest extends Specification {
         given:
         def config = new WaveConfig([enabled: true])
         expect:
-        config.toString() == 'WaveConfig(enabled:true, endpoint:https://wave.seqera.io, containerConfigUrl:[], tokensCacheMaxDuration:30m, condaOpts:CondaOpts(mambaImage=mambaorg/micromamba:1.5.8-lunar; basePackages=conda-forge::procps-ng, commands=null), spackOpts:SpackOpts(basePackages=null, commands=null), strategy:[container, dockerfile, conda, spack], bundleProjectResources:null, buildRepository:null, cacheRepository:null, retryOpts:RetryOpts(delay:450ms, maxDelay:1m 30s, maxAttempts:10, jitter:0.25), httpClientOpts:HttpOpts(), freezeMode:null, preserveFileTimestamp:null)'
+        config.toString() == 'WaveConfig(enabled:true, endpoint:https://wave.seqera.io, containerConfigUrl:[], tokensCacheMaxDuration:30m, condaOpts:CondaOpts(mambaImage=mambaorg/micromamba:1.5.10-noble; basePackages=conda-forge::procps-ng, commands=null), spackOpts:SpackOpts(basePackages=null, commands=null), strategy:[container, dockerfile, conda, spack], bundleProjectResources:null, buildRepository:null, cacheRepository:null, retryOpts:RetryOpts(delay:450ms, maxDelay:1m 30s, maxAttempts:10, jitter:0.25), httpClientOpts:HttpOpts(), freezeMode:null, preserveFileTimestamp:null, buildMaxDuration:40m, mirrorMode:null, scanMode:null, scanAllowedLevels:null)'
     }
 
-    def 'should not allow invalid settinga' () {
+    def 'should not allow invalid setting' () {
         when:
         new WaveConfig(endpoint: 'foo')
         then:
@@ -240,4 +242,38 @@ class WaveConfigTest extends Specification {
         config.preserveFileTimestamp()
     }
 
+    def 'should enabled mirror mode' () {
+        expect:
+        !new WaveConfig([:]).mirrorMode()
+        and:
+        new WaveConfig([mirror:true]).mirrorMode()
+    }
+
+    @Unroll
+    def 'should validate scan mode' () {
+        expect:
+        new WaveConfig(scan: [mode: MODE]).scanMode() == EXPECTED
+        where:
+        MODE        | EXPECTED
+        null        | null
+        'none'      | ScanMode.none
+        'async'     | ScanMode.async
+        'required'  | ScanMode.required
+    }
+
+    @Unroll
+    def 'should validate scan levels' () {
+        expect:
+        new WaveConfig(scan: [allowedLevels: LEVEL]).scanAllowedLevels() == EXPECTED
+        where:
+        LEVEL               | EXPECTED
+        null                | null
+        'low'               | List.of(ScanLevel.LOW)
+        'LOW'               | List.of(ScanLevel.LOW)
+        'low,high'          | List.of(ScanLevel.LOW,ScanLevel.HIGH)
+        'LOW, HIGH'         | List.of(ScanLevel.LOW,ScanLevel.HIGH)
+        ['medium','high']   | List.of(ScanLevel.MEDIUM,ScanLevel.HIGH)
+
+    }
+
 }
diff --git a/test-ci.sh b/test-ci.sh
index 41c008b53e..5444674369 100755
--- a/test-ci.sh
+++ b/test-ci.sh
@@ -9,17 +9,12 @@ X_PULL_REQUEST=${TRAVIS_PULL_REQUEST:-false}
 [[ $GITHUB_REF ]] && X_BRANCH=$(echo $GITHUB_REF | awk '{n=split($1,A,"/"); print A[n]}')
 [[ $GITHUB_EVENT_NAME == pull_request ]] && X_PULL_REQUEST=true
 
-if [ "$TEST_JDK" -ge 19 ]; then
-  export NXF_ENABLE_VIRTUAL_THREADS=true
-fi
-
 export WITH_DOCKER='-with-docker'
 export NXF_PLUGINS_DIR=$PWD/build/plugins
 export NXF_CMD=$PWD/nextflow;
 export TEST_JDK
 export TEST_MODE
 
-unset JAVA_TOOL_OPTIONS # this variable mess-up Capsule loader Java version parsing
 (
  $NXF_CMD info
  cd validation
diff --git a/test-e2e/.gitignore b/test-e2e/.gitignore
new file mode 100644
index 0000000000..53a548845f
--- /dev/null
+++ b/test-e2e/.gitignore
@@ -0,0 +1,3 @@
+.nextflow
+nextflow
+build-info.properties
diff --git a/test-e2e/Dockerfile b/test-e2e/Dockerfile
new file mode 100644
index 0000000000..eb8df06a67
--- /dev/null
+++ b/test-e2e/Dockerfile
@@ -0,0 +1,11 @@
+FROM amazoncorretto:17-al2023
+COPY .nextflow /.nextflow
+COPY nextflow /usr/bin/nextflow
+ENV NXF_HOME=/.nextflow
+RUN nextflow info
+RUN NXF_PLUGINS_DEFAULT=false nextflow plugin install xpack-amzn,xpack-google
+
+FROM scratch
+COPY --from=0 /.nextflow /.nextflow
+COPY --from=0 /usr/bin/nextflow /usr/bin/nextflow
+
diff --git a/test-e2e/run.sh b/test-e2e/run.sh
new file mode 100644
index 0000000000..4591606921
--- /dev/null
+++ b/test-e2e/run.sh
@@ -0,0 +1,89 @@
+#
+# Copyright 2013-2024, Seqera Labs
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+#
+
+# cleanup
+rm -rf .nextflow && mkdir .nextflow
+# copy nextflow dependencies
+(cd ..
+./gradlew compile assemble
+BUILD_PACK=1 ./gradlew installScratch publishToMavenLocal
+)
+
+# copy nextflow plugins
+cp -r ../build/plugins .nextflow/
+# copy nextflow launcher script
+cp ../nextflow . && chmod +x nextflow
+cp ../modules/nextflow/src/main/resources/META-INF/build-info.properties .
+source build-info.properties
+
+if [ -z "$version" ]; then
+    echo "Error: version is empty or missing"; exit 1
+fi
+if [ -z "$build" ]; then
+    echo "Error: build is empty or missing"; exit 1
+fi
+if [ -z "$commitId" ]; then
+    echo "Error: commitId is empty or missing"; exit 1
+fi
+
+#
+# build a scratch container image with assembled newxtflow runtime and plugins
+#
+tag=${version}-${commitId}
+base=${base:-'public.cr.seqera.io/platform/nf-launcher:j17-base'}
+repository=${repository:-'public.cr.seqera.io/snapshots/nextflow-scratch'}
+image=${repository}:${tag}
+
+docker buildx build \
+  --platform linux/amd64 \
+  --push \
+  --progress=plain \
+  --tag ${image} \
+  --build-arg TARGETPLATFORM=linux/amd64 \
+  .
+echo "Nextflow snapshots launcher image $image"
+
+#
+# Create an ephemeral container with the scratch image and base Platform launcher image
+#
+launcher=$(wave -i ${base} --include ${image} --config-env NXF_HOME=/.nextflow)
+echo "Running Platform tests using image launcher: $launcher"
+
+# determining the e2e test environment checking the $COMMIT_MESSAGE
+# that is set by GitHub action workflow. If it does not exist fallback
+# to the commit message in the git rpeo
+if [ -z "$COMMIT_MESSAGE" ]; then
+  COMMIT_MESSAGE=$(git show -s --format='%s')
+  echo "Commit message [from git]: $COMMIT_MESSAGE"
+else
+  echo "Commit message [from gha]: $COMMIT_MESSAGE"
+fi
+if echo "$COMMIT_MESSAGE" | grep -q "\[e2e prod\]"; then
+  ENVIRONMENT="production"
+else
+  ENVIRONMENT="staging"
+fi
+
+#
+# Finally launch the showcase automation
+# see https://github.com/seqeralabs/showcase-automation/
+echo "Launching seqera-showcase-${ENVIRONMENT}"
+gh workflow run \
+  seqera-showcase-${ENVIRONMENT}.yml \
+  --repo seqeralabs/showcase-automation \
+  -f launch_container=${launcher}
+
diff --git a/tests/checks/error-ignore-then-fail.nf/.checks b/tests/checks/error-ignore-then-fail.nf/.checks
index 688d88fb3e..6e91cd7067 100644
--- a/tests/checks/error-ignore-then-fail.nf/.checks
+++ b/tests/checks/error-ignore-then-fail.nf/.checks
@@ -8,5 +8,6 @@ set -e
 
 [ $status -ne 0 ] || false
 
-[[ `< .nextflow.log grep -c 'Submitted process > foo'` == 1 ]] || false
+[[ `< .nextflow.log grep -c 'Submitted process > foo'` == 3 ]] || false
+[[ `< .nextflow.log grep -c 'Submitted process > bar'` == 1 ]] || false
 [[ `< .nextflow.log grep -c 'Error is ignored'` == 1 ]] || false
diff --git a/tests/checks/error-ignore-then-fail.nf/.config b/tests/checks/error-ignore-then-fail.nf/.config
index ae0cd92bff..09a06e5e06 100644
--- a/tests/checks/error-ignore-then-fail.nf/.config
+++ b/tests/checks/error-ignore-then-fail.nf/.config
@@ -1 +1,6 @@
-workflow.failOnIgnore = true
+workflow {
+    failOnIgnore = true
+}
+process {
+  errorStrategy = 'ignore'
+}
diff --git a/tests/checks/run.sh b/tests/checks/run.sh
old mode 100644
new mode 100755
diff --git a/tests/checks/stub-retry.nf/.checks b/tests/checks/stub-retry.nf/.checks
new file mode 100644
index 0000000000..6a5c757beb
--- /dev/null
+++ b/tests/checks/stub-retry.nf/.checks
@@ -0,0 +1,11 @@
+set -e
+
+echo ''
+$NXF_RUN -stub | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > stubtest'` == 1 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Re-submitted process > stubtest'` == 1 ]] || false
+
+[[ `grep -c 'Stubbing. Creating file' stdout` == 1 ]] || false
+
+
diff --git a/tests/checks/trace-access.nf/.checks b/tests/checks/trace-access.nf/.checks
new file mode 100644
index 0000000000..887f37fd3b
--- /dev/null
+++ b/tests/checks/trace-access.nf/.checks
@@ -0,0 +1,11 @@
+set -e
+
+echo ''
+$NXF_RUN | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo'` == 1 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Re-submitted process > foo'` == 3 ]] || false
+
+[[ `grep -c 'mem: 8 GB (previous: 4294967296) (error: nextflow.exception.ProcessFailedException: Process .* terminated with an error exit status (137))' stdout` == 1 ]] || false
+
+
diff --git a/tests/error-ignore-then-fail.nf b/tests/error-ignore-then-fail.nf
index de2371e865..07cfa2b3e5 100644
--- a/tests/error-ignore-then-fail.nf
+++ b/tests/error-ignore-then-fail.nf
@@ -15,15 +15,39 @@
  * limitations under the License.
  */
 
+workflow {
+    input_channel = channel.of("SAMP1", "SAMP2", "SAMP3")
+    foo(input_channel)
+    bar(foo.out.sample_ids.collect())
+}
+
 process foo {
-    errorStrategy 'ignore'
+    input:
+    val sample_id
+
+    output:
+    val sample_id, emit: sample_ids
 
     script:
-    '''
-    exit 1
-    '''
+    """
+    if [[ $sample_id == "SAMP1" ]]; then
+        exit 2
+    fi
+    ls -lah .*
+    """
 }
 
-workflow {
-    foo()
+process bar {
+    input:
+    val ready
+
+    output:
+    stdout
+
+    script:
+    """
+    ls -lah .*
+    """
+
 }
+
diff --git a/tests/output-dsl.nf b/tests/output-dsl.nf
index 22d9cea365..f3ed165185 100644
--- a/tests/output-dsl.nf
+++ b/tests/output-dsl.nf
@@ -26,6 +26,7 @@ process align {
   path("*.bam")
   path("${x}.bai")
 
+  script:
   """
   echo ${x} > ${x}.bam
   echo ${x} | rev > ${x}.bai
@@ -40,6 +41,7 @@ process my_combine {
   output:
   path 'result.txt'
 
+  script:
   """
   cat $bamfile > result.txt
   cat $baifile >> result.txt
@@ -50,6 +52,7 @@ process foo {
   output:
   path 'xxx'
 
+  script:
   '''
   mkdir xxx
   touch xxx/A
@@ -59,13 +62,14 @@ process foo {
 }
 
 workflow {
-  def input = Channel.of('alpha','beta','delta')
+  main:
+  input = Channel.of('alpha','beta','delta')
   align(input)
 
-  def bam = align.out[0].toSortedList { it.name }
-  def bai = align.out[1].toSortedList { it.name }
-  my_combine( bam, bai )
-  my_combine.out.view{ it.text }
+  bams = align.out[0].toSortedList { bam -> bam.name }
+  bais = align.out[1].toSortedList { bai -> bai.name }
+  my_combine( bams, bais )
+  my_combine.out.view { it -> it.text }
 
   foo()
 
@@ -76,10 +80,8 @@ workflow {
 }
 
 output {
-  directory 'results'
-  mode 'copy'
-
   'data' {
+    path { val -> { file -> file } }
     index {
       path 'index.csv'
       mapper { val -> [filename: val] }
diff --git a/tests/stub-retry.nf b/tests/stub-retry.nf
new file mode 100644
index 0000000000..a682d899c4
--- /dev/null
+++ b/tests/stub-retry.nf
@@ -0,0 +1,30 @@
+process stubtest {
+    debug true
+    errorStrategy 'retry'
+
+    output:
+    path("*.txt")
+
+    script:
+    """
+    echo "Not stubbing"
+    touch script.txt
+    """
+
+    stub:
+    if( task.attempt < 2 ) {
+    """
+    echo "Stubbing. Not creating file"
+    """
+    } else {
+    """
+    echo "Stubbing. Creating file"
+    touch script.txt
+    """
+    }
+}
+
+workflow {
+    main:
+    stubtest()
+}
diff --git a/tests/trace-access.nf b/tests/trace-access.nf
new file mode 100644
index 0000000000..ff55dbdb84
--- /dev/null
+++ b/tests/trace-access.nf
@@ -0,0 +1,24 @@
+process foo {
+  memory { task.attempt > 1 ? task.previousTrace.memory * 2 : (1.GB) }
+  errorStrategy 'retry'
+  maxRetries 3
+  input:
+     val i
+  output:
+     stdout
+  script:
+  if( task.attempt <= 3 ){
+  """
+  exit 137
+  """
+  } else {
+  """
+  echo 'mem: $task.memory (previous: $task.previousTrace.memory) (error: $task.previousException)'
+  exit 0
+  """
+  }
+}
+
+workflow {
+  foo(channel.of(1)).view() 
+}
diff --git a/validation/awsbatch-unstage-fail.config b/validation/awsbatch-unstage-fail.config
new file mode 100644
index 0000000000..81b96579d7
--- /dev/null
+++ b/validation/awsbatch-unstage-fail.config
@@ -0,0 +1,12 @@
+/*
+ * do not include plugin requirements otherwise latest
+ * published version will be downloaded instead of using local build
+ */
+
+workDir = 's3://nextflow-ci/work'
+process.executor = 'awsbatch'
+process.queue = 'nextflow-ci'
+process.container = 'quay.io/nextflow/test-aws-unstage-fail:1.0'
+aws.region = 'eu-west-1'
+aws.batch.maxTransferAttempts = 3 
+aws.batch.delayBetweenAttempts = '5 sec'
diff --git a/validation/awsbatch.sh b/validation/awsbatch.sh
index d58727e7e8..b73571cbd6 100644
--- a/validation/awsbatch.sh
+++ b/validation/awsbatch.sh
@@ -7,6 +7,13 @@ get_abs_filename() {
 
 export NXF_CMD=${NXF_CMD:-$(get_abs_filename ../launch.sh)}
 
+# Execution should fail ignoring
+$NXF_CMD run test-aws-unstage-fail.nf -c awsbatch-unstage-fail.config || true
+[[ `grep -c "Error executing process > 'test (1)'" .nextflow.log` == 1 ]] || false
+[[ `grep -c "  Essential container in task exited" .nextflow.log` == 1 ]] || false
+[[ `grep -cozP "Command exit status:\n  1" .nextflow.log` == 1 ]] || false
+[[ `grep -c "Producing a failure in aws" .nextflow.log` == 2 ]] || false
+
 $NXF_CMD run test-complexpaths.nf -c awsbatch.config
 [[ -d foo ]] || false
 [[ -e 'foo/.alpha' ]] || false
@@ -73,4 +80,4 @@ $NXF_CMD run nextflow-io/hello \
     -process.array 10 \
     -with-wave \
     -with-fusion \
-    -c awsbatch.config
\ No newline at end of file
+    -c awsbatch.config
diff --git a/validation/google.sh b/validation/google.sh
index 8dcda8ab99..0dcb9606f8 100644
--- a/validation/google.sh
+++ b/validation/google.sh
@@ -6,9 +6,6 @@ get_abs_filename() {
 
 export NXF_CMD=${NXF_CMD:-$(get_abs_filename ../launch.sh)}
 
-echo $GOOGLE_SECRET | base64 -d > $PWD/google_credentials.json
-export GOOGLE_APPLICATION_CREDENTIALS=$PWD/google_credentials.json
-
 [[ $TOWER_ACCESS_TOKEN ]] && OPTS='-with-tower' || OPTS=''
 set -x
 
diff --git a/validation/test-aws-unstage-fail-container/Dockerfile b/validation/test-aws-unstage-fail-container/Dockerfile
new file mode 100644
index 0000000000..0dd281ba58
--- /dev/null
+++ b/validation/test-aws-unstage-fail-container/Dockerfile
@@ -0,0 +1,11 @@
+FROM ubuntu
+
+RUN apt-get update && apt-get -y install curl unzip && apt-get clean
+
+
+RUN curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip" && \
+    unzip awscliv2.zip && ./aws/install && rm -rf aws*
+
+ADD fake_aws /fake_aws
+
+ENV PATH=/fake_aws/bin/:$PATH
diff --git a/validation/test-aws-unstage-fail-container/fake_aws/bin/aws b/validation/test-aws-unstage-fail-container/fake_aws/bin/aws
new file mode 100755
index 0000000000..80985d9e08
--- /dev/null
+++ b/validation/test-aws-unstage-fail-container/fake_aws/bin/aws
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+if [[ "$*" == *".command."* ]] || [[ "$*" == *".exitcode"* ]]; then
+   /usr/local/bin/aws $@
+else
+   >&2 echo "Producing a failure in aws $@"
+   exit 2
+fi
+
diff --git a/validation/test-aws-unstage-fail.nf b/validation/test-aws-unstage-fail.nf
new file mode 100644
index 0000000000..96bcb9af1e
--- /dev/null
+++ b/validation/test-aws-unstage-fail.nf
@@ -0,0 +1,16 @@
+process test {
+  input: 
+	val i
+  output: 
+        file("test${i}")
+        file("test_2_${i}")
+  script:
+  """
+  dd if=/dev/urandom of=test${i} bs=1K count=90
+  dd if=/dev/urandom of=test_2_${i} bs=1K count=90
+  """
+}
+
+workflow {
+  Channel.of(1) | test
+}
diff --git a/validation/wave-tests/example6/nextflow.config b/validation/wave-tests/example6/nextflow.config
index f58834306f..c757b3bb7b 100644
--- a/validation/wave-tests/example6/nextflow.config
+++ b/validation/wave-tests/example6/nextflow.config
@@ -1,12 +1,3 @@
-process {
-  container = 'quay.io/nextflow/rnaseq-nf:v1.1'
-}
- 
-params {
-  reads = 's3://rnaseq-nf/data/ggal/lung_{1,2}.fq'
-  transcriptome = 's3://rnaseq-nf/data/ggal/transcript.fa'
-}
-
 docker {
   enabled = true
   envWhitelist = 'AWS_ACCESS_KEY_ID,AWS_SECRET_ACCESS_KEY'
@@ -16,5 +7,3 @@ fusion {
   enabled = true
 }
 
-workDir = 's3://nextflow-ci/wave'
-
diff --git a/validation/wave-tests/example6/run-aws.sh b/validation/wave-tests/example6/run-aws.sh
index b63724d33c..0f2d2247fa 100644
--- a/validation/wave-tests/example6/run-aws.sh
+++ b/validation/wave-tests/example6/run-aws.sh
@@ -1,6 +1,6 @@
 $NXF_CMD run \
     rnaseq-nf \
-    -profile batch \
+    -profile batch,s3-data \
     -with-wave \
     -with-fusion \
     -process.scratch false
diff --git a/validation/wave-tests/example6/run-gcp.sh b/validation/wave-tests/example6/run-gcp.sh
index b522ac13c5..c55dcdb3ec 100644
--- a/validation/wave-tests/example6/run-gcp.sh
+++ b/validation/wave-tests/example6/run-gcp.sh
@@ -1,6 +1,6 @@
 $NXF_CMD run \
     rnaseq-nf \
-    -profile gcb \
+    -profile google-batch,gs-data \
     -with-wave \
     -with-fusion \
     -process.scratch false
diff --git a/validation/wave-tests/example6/run.sh b/validation/wave-tests/example6/run.sh
index 0bb6d254c5..971a65f351 100644
--- a/validation/wave-tests/example6/run.sh
+++ b/validation/wave-tests/example6/run.sh
@@ -1,2 +1,5 @@
-$NXF_CMD run rnaseq-nf -with-wave
+$NXF_CMD run \
+    rnaseq-nf \
+    -with-wave \
+    -w s3://nextflow-ci/wave
 
diff --git a/validation/wave.sh b/validation/wave.sh
index 6b8953a7f3..b24b718be6 100644
--- a/validation/wave.sh
+++ b/validation/wave.sh
@@ -25,4 +25,4 @@ echo "Test Wave running rnaseq-nf with Fusion on AWS Batch"
 (cd wave-tests/example6; bash run-aws.sh)
 
 echo "Test Wave running rnaseq-nf with Fusion on Google Batch"
-(cd wave-tests/example6; bash run-aws.sh)
+(cd wave-tests/example6; bash run-gcp.sh)