Merge pull request #3324 from nf-core/dev

Dev -> main for 3.1.0

Author: mashehu

.github/actions/create-lint-wf/action.yml

@@ -15,7 +15,6 @@ runs:
         cd create-lint-wf
         export NXF_WORK=$(pwd)
 
-    # Set up Nextflow
     - name: Install Nextflow
       uses: nf-core/setup-nextflow@v2
       with:
@@ -65,6 +64,12 @@ runs:
       run: find nf-core-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
       working-directory: create-lint-wf
 
+    # Add empty ro-crate file
+    - name: add empty ro-crate file
+      shell: bash
+      run: touch nf-core-testpipeline/ro-crate-metadata.json
+      working-directory: create-lint-wf
+
     # Run nf-core pipelines linting
     - name: nf-core pipelines lint
       shell: bash

.github/workflows/create-lint-wf.yml

@@ -27,14 +27,12 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
-env:
-  NXF_ANSI_LOG: false
-
 jobs:
   MakeTestWorkflow:
     runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
     env:
       NXF_ANSI_LOG: false
+
     strategy:
       matrix:
         NXF_VER:

.github/workflows/create-test-lint-wf-template.yml

@@ -51,6 +51,7 @@ jobs:
     needs: prepare-matrix
     env:
       NXF_ANSI_LOG: false
+
     strategy:
       matrix:
         TEMPLATE: ${{ fromJson(needs.prepare-matrix.outputs.all_features) }}
@@ -147,6 +148,11 @@ jobs:
         run: find my-prefix-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
         working-directory: create-test-lint-wf
 
+      # Add empty ro-crate file
+      - name: add empty ro-crate file
+        run: touch my-prefix-testpipeline/ro-crate-metadata.json
+        working-directory: create-test-lint-wf
+
       # Run nf-core linting
       - name: nf-core pipelines lint
         run: nf-core --log-file log.txt --hide-progress pipelines lint --dir my-prefix-testpipeline --fail-warned

.github/workflows/create-test-wf.yml

@@ -27,15 +27,13 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
-env:
-  NXF_ANSI_LOG: false
-
 jobs:
   RunTestWorkflow:
     # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
     runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
     env:
       NXF_ANSI_LOG: false
+
     strategy:
       matrix:
         NXF_VER:

.github/workflows/pytest.yml

@@ -132,7 +132,7 @@ jobs:
 
       - name: Test with pytest
         run: |
-          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --durations=0 && exit_code=0|| exit_code=$?
+          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --cov-config=.coveragerc --durations=0 && exit_code=0|| exit_code=$?
           # don't fail if no tests were collected, e.g. for test_licence.py
           if [ "${exit_code}" -eq 5 ]; then
             echo "No tests were collected"

.gitpod.yml

@@ -1,4 +1,4 @@
-image: nfcore/gitpod:dev
+image: nfcore/gitpod:latest
 tasks:
   - name: install current state of nf-core/tools and setup pre-commit
     command: |
@@ -9,11 +9,4 @@ tasks:
 
 vscode:
   extensions:
-    - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
-    - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
-    - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
-    - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
-    - nextflow.nextflow # Nextflow syntax highlighting
-    - oderwat.indent-rainbow # Highlight indentation level
-    - streetsidesoftware.code-spell-checker # Spelling checker for source code
-    - charliermarsh.ruff # Code linter Ruff
+    - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.4
+    rev: v0.8.2
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix

.vscode/settings.json

@@ -0,0 +1,9 @@
+{
+    "python.testing.pytestEnabled": true,
+    "python.testing.unittestEnabled": false,
+    "python.testing.nosetestsEnabled": false,
+    "python.testing.pytestArgs": ["tests", "-v", "--tb=short"],
+    "python.testing.autoTestDiscoverOnSaveEnabled": true,
+    "python.terminal.activateEnvInCurrentTerminal": true,
+    "python.terminal.shellIntegration.enabled": true
+}

CHANGELOG.md

@@ -1,49 +1,77 @@
 # nf-core/tools: Changelog
 
-## v3.0.3dev
+## [v3.1.0 - Brass Boxfish](https://github.com/nf-core/tools/releases/tag/3.1.0) - [2024-12-09]
+
+**Highlights**
+
+- We added the new `contributors` field to the pipeline template `manifest`.
+- The `nf-core pipelines download` command supports ORAS container URIs.
+- New command `nf-core subworkflows patch`.
 
 ### Template
 
 - Keep pipeline name in version.yml file ([#3223](https://github.com/nf-core/tools/pull/3223))
 - Fix Manifest DOI text ([#3224](https://github.com/nf-core/tools/pull/3224))
 - Do not assume pipeline name is url ([#3225](https://github.com/nf-core/tools/pull/3225))
-- fix workflow_dispatch trigger and parse more review comments in awsfulltest ([#3235](https://github.com/nf-core/tools/pull/3235))
+- fix `workflow_dispatch` trigger and parse more review comments in awsfulltest ([#3235](https://github.com/nf-core/tools/pull/3235))
 - Add resource limits to Gitpod profile([#3255](https://github.com/nf-core/tools/pull/3255))
 - Fix a typo ([#3268](https://github.com/nf-core/tools/pull/3268))
+- Remove `def` from `nextflow.config` and add `trace_report_suffix` param ([#3296](https://github.com/nf-core/tools/pull/3296))
+- Move `includeConfig 'conf/modules.config'` next to `includeConfig 'conf/base.config'` to not overwrite tests profiles configurations ([#3301](https://github.com/nf-core/tools/pull/3301))
+- Use `params.monochrome_logs` in the template and update nf-core components ([#3310](https://github.com/nf-core/tools/pull/3310))
+- Fix some typos and improve writing in `usage.md` and `CONTRIBUTING.md` ([#3302](https://github.com/nf-core/tools/pull/3302))
+- Add `manifest.contributors` to `nextflow.config` ([#3311](https://github.com/nf-core/tools/pull/3311))
+- Update template components ([#3328](https://github.com/nf-core/tools/pull/3328))
+- Template: Remove mention of GRCh37 if igenomes is skipped ([#3330](https://github.com/nf-core/tools/pull/3330))
 
 ### Download
 
-- First steps towards fixing [#3179](https://github.com/nf-core/tools/issues/3179): Modify `prioritize_direct_download()` to retain Seqera Singularity https:// Container URIs and hardcode Seqera Containers into `gather_registries()` ([#3244](https://github.com/nf-core/tools/pull/3244)).
+- First steps towards fixing [#3179](https://github.com/nf-core/tools/issues/3179): Modify `prioritize_direct_download()` to retain Seqera Singularity `https://` Container URIs and hardcode Seqera Containers into `gather_registries()` ([#3244](https://github.com/nf-core/tools/pull/3244)).
+- Further steps towards fixing [#3179](https://github.com/nf-core/tools/issues/3179): Enable limited support for `oras://` container paths (_only absolute URIs, no flexible registries like with Docker_) and prevent unnecessary image downloads for Seqera Container modules with `reconcile_seqera_container_uris()` ([#3293](https://github.com/nf-core/tools/pull/3293)).
+- Update dawidd6/action-download-artifact action to v7 ([#3306](https://github.com/nf-core/tools/pull/3306))
 
 ### Linting
 
-- General: Run pre-commit when testing linting the template pipeline ([#3280](https://github.com/nf-core/tools/pull/3280))
+- allow mixed `str` and `dict` entries in lint config ([#3228](https://github.com/nf-core/tools/pull/3228))
+- fix `meta_yml` linting test failing due to `module.process_name` always being `""` ([#3317](https://github.com/nf-core/tools/pull/3317))
+- fix module section regex matching wrong things ([#3321](https://github.com/nf-core/tools/pull/3321))
 
 ### Modules
 
 - add a panel around diff previews when updating ([#3246](https://github.com/nf-core/tools/pull/3246))
 
 ### Subworkflows
 
+- Add `nf-core subworkflows patch` command ([#2861](https://github.com/nf-core/tools/pull/2861))
+- Improve subworkflow nf-test migration warning ([#3298](https://github.com/nf-core/tools/pull/3298))
+
 ### General
 
-- Include .nf-core.yml in `nf-core pipelines bump-version` ([#3220](https://github.com/nf-core/tools/pull/3220))
+- Include `.nf-core.yml` in `nf-core pipelines bump-version` ([#3220](https://github.com/nf-core/tools/pull/3220))
 - create: add shortcut to toggle all switches ([#3226](https://github.com/nf-core/tools/pull/3226))
 - Remove unrelated values when saving `.nf-core` file ([#3227](https://github.com/nf-core/tools/pull/3227))
-- chore(deps): update pre-commit hook pre-commit/mirrors-mypy to v1.12.0 ([#3230](https://github.com/nf-core/tools/pull/3230))
-- chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.7.0 ([#3229](https://github.com/nf-core/tools/pull/3229))
-- Update python:3.12-slim Docker digest to 032c526 ([#3232](https://github.com/nf-core/tools/pull/3232))
 - use correct `--profile` options for `nf-core subworkflows test` ([#3233](https://github.com/nf-core/tools/pull/3233))
 - Update GitHub Actions ([#3237](https://github.com/nf-core/tools/pull/3237))
 - add `--dir/-d` option to schema commands ([#3247](https://github.com/nf-core/tools/pull/3247))
-- Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.1 ([#3250](https://github.com/nf-core/tools/pull/3250))
+- fix headers in api docs ([#3323](https://github.com/nf-core/tools/pull/3323))
 - handle new schema structure in `nf-core pipelines create-params-file` ([#3276](https://github.com/nf-core/tools/pull/3276))
 - Update Gitpod image to use Miniforge instead of Miniconda([#3274](https://github.com/nf-core/tools/pull/3274))
-- Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.3 ([#3275](https://github.com/nf-core/tools/pull/3275))
 - Add hint to solve git errors with a synced repo ([#3279](https://github.com/nf-core/tools/pull/3279))
-- Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.4 ([#3282](https://github.com/nf-core/tools/pull/3282))
+- Run pre-commit when testing linting the template pipeline ([#3280](https://github.com/nf-core/tools/pull/3280))
+- Make CLI prompt less nf-core specific ([#3326](https://github.com/nf-core/tools/pull/3326))
+- Update gitpod vscode extensions to use nf-core extension pack ([#3327](https://github.com/nf-core/tools/pull/3327))
+- Remove toList() channel operation from inside onComplete block ([#3304](https://github.com/nf-core/tools/pull/3304))
+- build: Setup VS Code tests ([#3292](https://github.com/nf-core/tools/pull/3292))
+- Don't break gitpod.yml with template string ([#3332](https://github.com/nf-core/tools/pull/3332))
+- rocrate: remove duplicated entries for name and version ([#3333](https://github.com/nf-core/tools/pull/3333))
+- rocrate: Update crate with version bump and handle new contributor field ([#3334](https://github.com/nf-core/tools/pull/3334))
+
+### Version updates
+
+- chore(deps): update pre-commit hook pre-commit/mirrors-mypy to v1.12.0 ([#3230](https://github.com/nf-core/tools/pull/3230))
 - Update codecov/codecov-action action to v5 ([#3283](https://github.com/nf-core/tools/pull/3283))
-- Update python:3.12-slim Docker digest to 2a6386a ([#3284](https://github.com/nf-core/tools/pull/3284))
+- Update gitpod/workspace-base Docker digest to 12853f7 ([#3309](https://github.com/nf-core/tools/pull/3309))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.2 ([#3325](https://github.com/nf-core/tools/pull/3325))
 
 ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11]
 

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.12-slim@sha256:2a6386ad2db20e7f55073f69a98d6da2cf9f168e05e7487d2670baeb9b7601c5
+FROM python:3.12-slim@sha256:2b0079146a74e23bf4ae8f6a28e1b484c6292f6fb904cbb51825b4a19812fcd8
 LABEL authors="[email protected],[email protected]" \
     description="Docker image containing requirements for nf-core/tools"
 

docs/api/_src/api/pipelines/bump_version.md

@@ -1,4 +1,4 @@
-# nf_core.bump_version
+# nf_core.pipelines.bump_version
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.bump_version

docs/api/_src/api/pipelines/create.md

@@ -1,4 +1,4 @@
-# nf_core.create
+# nf_core.pipelines.create
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.create

docs/api/_src/api/pipelines/download.md

@@ -1,4 +1,4 @@
-# nf_core.download
+# nf_core.pipelines.download
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.download

docs/api/_src/api/pipelines/launch.md

@@ -1,4 +1,4 @@
-# nf_core.launch
+# nf_core.pipelines.launch
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.launch

docs/api/_src/api/pipelines/lint.md

@@ -1,4 +1,4 @@
-# nf_core.lint
+# nf_core.pipelines.lint
 
 :::{seealso}
 See the [Lint Tests](/docs/nf-core-tools/api_reference/dev/pipeline_lint_tests) docs for information about specific linting functions.

docs/api/_src/api/pipelines/list.md

@@ -1,4 +1,4 @@
-# nf_core.list
+# nf_core.pipelines.list
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.list

docs/api/_src/api/pipelines/params-file.md

@@ -1,4 +1,4 @@
-# nf_core.params_file
+# nf_core.pipelines.params_file
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.params_file

docs/api/_src/api/pipelines/schema.md

@@ -1,4 +1,4 @@
-# nf_core.schema
+# nf_core.pipelines.schema
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.schema

docs/api/_src/api/pipelines/sync.md

@@ -1,4 +1,4 @@
-# nf_core.sync
+# nf_core.pipelines.sync
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.sync

docs/api/_src/api/pipelines/utils.md

@@ -1,4 +1,4 @@
-# nf_core.utils
+# nf_core.pipelines.utils
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.utils