Merge branch 'master' into test-plat-794

.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

VERSION

@@ -1 +1 @@
-24.10.0
+24.11.0-edge

build.gradle

@@ -109,8 +109,8 @@ allprojects {
 
         // Documentation required libraries
         groovyDoc 'org.fusesource.jansi:jansi:2.4.0'
-        groovyDoc "org.apache.groovy:groovy-groovydoc:4.0.23"
-        groovyDoc "org.apache.groovy:groovy-ant:4.0.23"
+        groovyDoc "org.apache.groovy:groovy-groovydoc:4.0.24"
+        groovyDoc "org.apache.groovy:groovy-ant:4.0.24"
     }
 
     test {

changelog.txt

@@ -1,5 +1,46 @@
 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 [email protected] [2b653b07]
+- Bump [email protected] [6af7198d]
+- Bump [email protected] [9494f970]
+- Bump [email protected] [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]

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"]

docs/aws.md

@@ -539,7 +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

docs/azure.md

@@ -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.
 

modules/nextflow/build.gradle

@@ -21,11 +21,11 @@ dependencies {
     api(project(':nf-commons'))
     api(project(':nf-httpfs'))
     api "org.apache.groovy:groovy:4.0.24"
-    api "org.apache.groovy:groovy-nio:4.0.23"
-    api "org.apache.groovy:groovy-xml:4.0.23"
-    api "org.apache.groovy:groovy-json:4.0.23"
-    api "org.apache.groovy:groovy-templates:4.0.23"
-    api "org.apache.groovy:groovy-yaml:4.0.23"
+    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"
@@ -53,7 +53,7 @@ dependencies {
     testImplementation 'org.subethamail:subethasmtp:3.1.7'
 
     // test configuration
-    testFixturesApi ("org.apache.groovy:groovy-test:4.0.23") { exclude group: 'org.apache.groovy' }
+    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' }

modules/nextflow/src/main/resources/META-INF/build-info.properties

@@ -1,4 +1,4 @@
-build=5928
-version=24.10.0
-timestamp=1730054192154
-commitId=6524d8dc9
+build=5929
+version=24.11.0-edge
+timestamp=1733218258400
+commitId=7e2c8d82b

modules/nextflow/src/main/resources/META-INF/plugins-info.txt

@@ -1,8 +1,8 @@
-nf-amazon@2.9.0
-nf-azure@1.10.1
+nf-amazon@2.10.0
+nf-azure@1.11.0
 [email protected]
 [email protected]
 [email protected]
-nf-google@1.15.2
+nf-google@1.16.0
 [email protected]
-nf-wave@1.7.2
+nf-wave@1.8.0

modules/nextflow/src/main/resources/nextflow/dag/mermaid.dag.template.html

@@ -19,6 +19,20 @@
 </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">

modules/nf-commons/build.gradle

@@ -27,7 +27,7 @@ sourceSets {
 dependencies {
     api "ch.qos.logback:logback-classic:1.4.14"
     api "org.apache.groovy:groovy:4.0.24"
-    api "org.apache.groovy:groovy-nio:4.0.23"
+    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'

modules/nf-httpfs/build.gradle

@@ -31,11 +31,11 @@ dependencies {
     api project(':nf-commons')
     api "ch.qos.logback:logback-classic:1.4.14"
     api "org.apache.groovy:groovy:4.0.24"
-    api "org.apache.groovy:groovy-nio:4.0.23"
+    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:4.0.23" // 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' }
 

nextflow

@@ -15,7 +15,7 @@
 #  limitations under the License.
 
 [[ "$NXF_DEBUG" == 'x' ]] && set -x
-NXF_VER=${NXF_VER:-'24.10.0'}
+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'}

nextflow.md5

@@ -1 +1 @@
-7dfd8066370310bff610aa209c988b3e
+66995c4139ebcd17bf99f17d9dd030d1

nextflow.sha1

@@ -1 +1 @@
-c142828a82fa6678a5af978d3545bb7f56072be6
+cdbb67bdb21c0e63fb48aabb8b168c12a31fa5b3

nextflow.sha256

@@ -1 +1 @@
-e848918fb9b85762822c078435d9ff71979a88cccff81ce5babd75d5eee52fe6
+69a86852c52dcfa7662407c46d16f05bd3dec16e0c505c2a2f71ccc56219d631

plugins/nf-amazon/build.gradle

@@ -60,5 +60,5 @@ dependencies {
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation project(':nextflow')
     testImplementation "org.apache.groovy:groovy:4.0.24"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.23"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.24"
 }

plugins/nf-azure/build.gradle

@@ -53,5 +53,5 @@ dependencies {
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation project(':nextflow')
     testImplementation "org.apache.groovy:groovy:4.0.24"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.23"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.24"
 }

plugins/nf-cloudcache/build.gradle

@@ -36,6 +36,6 @@ dependencies {
 
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation "org.apache.groovy:groovy:4.0.24"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.23"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.24"
 }
 

plugins/nf-codecommit/build.gradle

@@ -43,5 +43,5 @@ dependencies {
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation project(':nextflow')
     testImplementation "org.apache.groovy:groovy:4.0.24"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.23"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.24"
 }

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:4.0.23")  { 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:4.0.24"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.23"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.24"
 }
 

plugins/nf-google/build.gradle

@@ -47,7 +47,7 @@ dependencies {
 
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation "org.apache.groovy:groovy:4.0.24"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.23"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.24"
 }
 
 test {

plugins/nf-tower/build.gradle

@@ -38,5 +38,5 @@ dependencies {
 
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation "org.apache.groovy:groovy:4.0.24"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.23"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.24"
 }

plugins/nf-wave/build.gradle

@@ -41,5 +41,5 @@ dependencies {
 
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation "org.apache.groovy:groovy:4.0.24"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.23"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.24"
 }