Merge branch 'dev' into renovate/python-3.11-slim

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

@@ -0,0 +1,108 @@
+name: "Create and lint nf-core pipeline"
+description: "Create and lint nf-core pipeline"
+inputs:
+ NXF_VER:
+ description: "Nextflow version"
+ required: true
+
+runs:
+ using: "composite"
+ steps:
+ - name: go to subdirectory and change nextflow workdir
+ shell: bash
+ run: |
+ mkdir -p create-lint-wf
+ cd create-lint-wf
+ export NXF_WORK=$(pwd)
+
+ # Set up Nextflow
+ - name: Install Nextflow
+ uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+ with:
+ version: ${{ matrix.NXF_VER }}
+
+ # Build a pipeline from the template
+ - name: nf-core create
+ shell: bash
+ run: |
+ mkdir -p create-lint-wf && cd create-lint-wf
+ export NXF_WORK=$(pwd)
+ nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
+
+ # Try syncing it before we change anything
+ - name: nf-core sync
+ shell: bash
+ run: nf-core --log-file log.txt sync --dir nf-core-testpipeline/
+ working-directory: create-lint-wf
+
+ # Run code style linting
+ - name: run pre-commit
+ shell: bash
+ run: pre-commit run --all-files
+ working-directory: create-lint-wf
+
+ # Update modules to the latest version
+ - name: nf-core modules update
+ shell: bash
+ run: nf-core --log-file log.txt modules update --dir nf-core-testpipeline --all --no-preview
+ working-directory: create-lint-wf
+
+ # Remove TODO statements
+ - name: remove TODO
+ shell: bash
+ run: find nf-core-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \;
+ working-directory: create-lint-wf
+
+ # Replace zenodo.XXXXXX to pass readme linting
+ - name: replace zenodo.XXXXXX
+ shell: bash
+ run: find nf-core-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
+ working-directory: create-lint-wf
+
+ # Run nf-core linting
+ - name: nf-core lint
+ shell: bash
+ run: nf-core --verbose --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned
+ working-directory: create-lint-wf
+
+ - name: nf-core bump-version to release
+ shell: bash
+ run: nf-core --log-file log.txt bump-version --dir nf-core-testpipeline/ 1.1
+ working-directory: create-lint-wf
+
+ - name: nf-core lint in release mode
+ shell: bash
+ run: nf-core --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned --release
+ working-directory: create-lint-wf
+
+ - name: Upload log file artifact
+ if: ${{ always() }}
+ uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+ with:
+ name: nf-core-log-file-${{ matrix.NXF_VER }}
+ path: create-lint-wf/log.txt
+
+ - name: nf-core modules install
+ shell: bash
+ run: nf-core --log-file log.txt modules install fastqc --dir nf-core-testpipeline/ --force
+ working-directory: create-lint-wf
+
+ - name: nf-core modules install gitlab
+ shell: bash
+ run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git --branch branch-tester install fastp --dir nf-core-testpipeline/
+ working-directory: create-lint-wf
+
+ - name: nf-core modules list local
+ shell: bash
+ run: nf-core --log-file log.txt modules list local --dir nf-core-testpipeline/
+ working-directory: create-lint-wf
+
+ - name: nf-core modules list remote
+ shell: bash
+ run: nf-core --log-file log.txt modules list remote
+ working-directory: create-lint-wf
+
+ - name: nf-core modules list remote gitlab
+ shell: bash
+ run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git list remote
+ working-directory: create-lint-wf

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

@@ -3,6 +3,9 @@ on:
  push:
  branches:
  - dev
+ paths-ignore:
+ - "docs/**"
+ - "CHANGELOG.md"
  pull_request:
  release:
  types: [published]
@@ -57,101 +60,30 @@ jobs:
  python -m pip install --upgrade pip
  pip install .
 
- # Set up Nextflow
- - name: Install Nextflow
- uses: nf-core/setup-nextflow@dccbf847604cbc34610280d79644a02035d924ac # v1
+ - name: run create-lint-wf
+ uses: ./.github/actions/create-lint-wf
  with:
- version: ${{ matrix.NXF_VER }}
-
- # Build a pipeline from the template
- - name: nf-core create
- run: |
- mkdir create-lint-wf && cd create-lint-wf
- export NXF_WORK=$(pwd)
- nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
-
- # Try syncing it before we change anything
- - name: nf-core sync
- run: nf-core --log-file log.txt sync --dir nf-core-testpipeline/
- working-directory: create-lint-wf
+ NXF_VER: ${{ matrix.NXF_VER }}
 
  # Build a module from the template
  - name: nf-core modules create
- run: nf-core --log-file log.txt modules create bpipe --dir nf-core-testpipeline --author @nf-core-bot --label process_low --meta
- working-directory: create-lint-wf
-
- # Run code style linting
- - name: run pre-commit
- run: pre-commit run --all-files
- working-directory: create-lint-wf
-
- # Update modules to the latest version
- - name: nf-core modules update
- run: nf-core --log-file log.txt modules update --dir nf-core-testpipeline --all --no-preview
+ run: nf-core --verbose --log-file log.txt modules create bpipe --dir nf-core-testpipeline --author @nf-core-bot --label process_low --meta
  working-directory: create-lint-wf
 
  # Remove TODO statements
  - name: remove TODO
  run: find nf-core-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \;
  working-directory: create-lint-wf
 
- # Replace zenodo.XXXXXX to pass readme linting
- - name: replace zenodo.XXXXXX
- run: find nf-core-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
- working-directory: create-lint-wf
-
- # Run nf-core linting
- - name: nf-core lint
- run: nf-core --verbose --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned
- working-directory: create-lint-wf
-
  # Run the other nf-core commands
  - name: nf-core list
  run: nf-core --log-file log.txt list
  working-directory: create-lint-wf
 
- # - name: nf-core licences
- # run: nf-core --log-file log.txt licences nf-core-testpipeline
-
  - name: nf-core schema
  run: nf-core --log-file log.txt schema build --dir nf-core-testpipeline/ --no-prompts
  working-directory: create-lint-wf
 
- - name: nf-core bump-version
- run: nf-core --log-file log.txt bump-version --dir nf-core-testpipeline/ 1.1
- working-directory: create-lint-wf
-
- - name: nf-core lint in release mode
- run: nf-core --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned --release
- working-directory: create-lint-wf
-
- - name: nf-core modules install
- run: nf-core --log-file log.txt modules install fastqc --dir nf-core-testpipeline/ --force
- working-directory: create-lint-wf
-
- - name: nf-core modules install gitlab
- run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git --branch branch-tester install fastp --dir nf-core-testpipeline/
- working-directory: create-lint-wf
-
- - name: nf-core modules list local
- run: nf-core --log-file log.txt modules list local --dir nf-core-testpipeline/
- working-directory: create-lint-wf
-
- - name: nf-core modules list remote
- run: nf-core --log-file log.txt modules list remote
- working-directory: create-lint-wf
-
- - name: nf-core modules list remote gitlab
- run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git list remote
- working-directory: create-lint-wf
-
- - name: Upload log file artifact
- if: ${{ always() }}
- uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
- with:
- name: nf-core-log-file-${{ matrix.NXF_VER }}
- path: create-lint-wf/log.txt
-
  - name: Cleanup work directory
  run: sudo rm -rf create-lint-wf
  if: always()

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

@@ -3,6 +3,9 @@ on:
  push:
  branches:
  - dev
+ paths-ignore:
+ - "docs/**"
+ - "CHANGELOG.md"
  paths:
  - nf_core/pipeline-template/**
  pull_request:

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

@@ -3,6 +3,9 @@ on:
  push:
  branches:
  - dev
+ paths-ignore:
+ - "docs/**"
+ - "CHANGELOG.md"
  pull_request:
  release:
  types: [published]

.github/workflows/pytest.yml

@@ -12,6 +12,7 @@ on:
  paths-ignore:
  - "docs/**"
  - "CHANGELOG.md"
+ - ".github/**"
  release:
  types: [published]
  workflow_dispatch:

.github/workflows/update_components_template.yml

@@ -0,0 +1,46 @@
+name: Update Modules Template
+
+on:
+ schedule:
+ - cron: "0 0 * * *"
+ workflow_dispatch:
+
+jobs:
+ update_modules:
+ runs-on: ubuntu-latest
+
+ steps:
+ - name: Checkout repository
+ uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+
+ - name: Set up Python
+ uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+ with:
+ python-version: "3.x"
+
+ - name: Install nf-core
+ run: pip install nf-core
+
+ - name: Update modules
+ run: nf-core modules update --all
+ working-directory: nf-core/pipeline-template
+
+ - name: Update subworkflows
+ run: nf-core subworkflows update --all
+ working-directory: nf-core/pipeline-template
+
+ # Commit the changes
+ - name: Commit changes
+ run: |
+ git config user.email "core@nf-co.re"
+ git config user.name "nf-core-bot"
+ git add .
+ git status
+ git commit -m "[automated] Fix code linting"
+
+ # Open a new PR to dev with the changes
+ - name: Create PR
+ run: |
+ git checkout -b update-modules
+ git push origin update-modules
+ gh pr create --title "Update modules in template" --body "This PR updates the modules in the pipeline template" --base dev --head update-modules

CHANGELOG.md

@@ -9,6 +9,8 @@
 
 ### Linting
 
+- make creat-lint-wf composable ([#2733](https://github.com/nf-core/tools/pull/2733))
+
 ### Modules
 
 ### General
@@ -18,6 +20,7 @@
 - Update codecov/codecov-action digest to e0b68c6 ([#2728](https://github.com/nf-core/tools/pull/2728))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.2.1 ([#2730](https://github.com/nf-core/tools/pull/2730))
 - Update python:3.11-slim Docker digest to 2a746e2 ([#2743](https://github.com/nf-core/tools/pull/2743))
+- Update actions/setup-python action to v5 ([#2739](https://github.com/nf-core/tools/pull/2739))
 
 ## [v2.12.1 - Aluminium Wolf - Patch](https://github.com/nf-core/tools/releases/tag/2.12.1) - [2024-02-01]
 

nf_core/lint/multiqc_config.py

@@ -9,6 +9,7 @@ def multiqc_config(self) -> Dict[str, List[str]]:
  Basic template:
 
  .. code-block:: yaml
+
  report_comment: >
  This report has been generated by the <a href="https://github.com/nf-core/quantms" target="_blank">nf-core/quantms</a>
  analysis pipeline. For information about how to interpret these results, please see the
@@ -18,8 +19,8 @@ def multiqc_config(self) -> Dict[str, List[str]]:
  order: -1000
  nf-core-quantms-summary:
  order: -1001
-
  export_plots: true
+
  """
  passed: List[str] = []
  failed: List[str] = []

nf_core/pipeline-template/.github/workflows/download_pipeline.yml

@@ -47,13 +47,13 @@ jobs:
  run: |
  echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
  echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
- echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
+ echo "{% raw %}REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
 
  - name: Download the pipeline
  env:
  NXF_SINGULARITY_CACHEDIR: ./
  run: |
- nf-core download {% raw %} ${{ env.REPO_LOWERCASE }} \
+ nf-core download ${{ env.REPO_LOWERCASE }} \
  --revision ${{ env.REPO_BRANCH }} \
  --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
  --compress "none" \