Update pre-commit hooks #27612
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| name: Run Linting | |
| on: | |
| push: | |
| branches: | |
| # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging | |
| - "renovate/**" # branches Renovate creates | |
| pull_request: | |
| branches: [master] | |
| merge_group: | |
| types: [checks_requested] | |
| branches: [master] | |
| workflow_dispatch: | |
| inputs: | |
| runners: | |
| description: "Runners to test on" | |
| type: choice | |
| options: | |
| - "ubuntu-latest" | |
| - "self-hosted" | |
| default: "self-hosted" | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver | |
| NXF_VER: "26.04.0" | |
| NXF_SYNTAX_PARSER: "v2" | |
| jobs: | |
| pre-commit: | |
| runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} | |
| steps: | |
| - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 | |
| - uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 | |
| - name: Run prek | |
| uses: j178/prek-action@4e14d07f9231acabce116ccfca13b13dd9755ece # v3.0.0 | |
| ################### | |
| # nf-core linting # | |
| ################### | |
| # TODO Move these to pre-commit | |
| # https://github.com/nf-core/tools/pull/3141 | |
| nf-core-changes: | |
| name: nf-core-changes | |
| runs-on: | |
| - runs-on=${{ github.run_id }}-nf-core-changes | |
| - runner=4cpu-linux-x64 | |
| - image=ubuntu22-full-x64 | |
| outputs: | |
| # https://github.com/dorny/paths-filter?tab=readme-ov-file#custom-processing-of-changed-files | |
| modules: ${{ steps.filter.outputs.modules }} | |
| modules_files: ${{ steps.module_names.outputs.result }} | |
| subworkflows: ${{ steps.filter.outputs.subworkflows }} | |
| subworkflows_files: ${{ steps.subworkflow_names.outputs.result }} | |
| steps: | |
| - name: Clean workspace | |
| run: | | |
| sudo rm -rf ./* || true | |
| sudo rm -rf ./.* || true | |
| - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 | |
| with: | |
| fetch-depth: 2 # To retrieve the preceding commit. | |
| - uses: dorny/paths-filter@ceb8a2b8f2d89434be7ff52d3de7ec3738c5cc9d # v4 | |
| id: filter | |
| with: | |
| filters: | | |
| modules: | |
| - added|modified: 'modules/nf-core/**' | |
| subworkflows: | |
| - added|modified: 'subworkflows/nf-core/**' | |
| token: "" | |
| list-files: "json" | |
| - name: Get module name | |
| uses: actions/github-script@3a2844b7e9c422d3c10d287c895573f7108da1b3 # v9 | |
| id: module_names | |
| with: | |
| script: | | |
| return [...new Set(${{ steps.filter.outputs.modules_files }} | |
| .filter(x => x.endsWith('main.nf') || x.endsWith('.nf.test.snap')) | |
| .map(path => path | |
| .replace('modules/nf-core/', '') | |
| .replace(/\/(main\.nf|tests\/.*)$/, '') | |
| ) | |
| )]; | |
| - name: Get subworkflow name | |
| uses: actions/github-script@3a2844b7e9c422d3c10d287c895573f7108da1b3 # v9 | |
| id: subworkflow_names | |
| with: | |
| script: | | |
| return [...new Set(${{ steps.filter.outputs.subworkflows_files }} | |
| .filter(x => x.endsWith('main.nf') || x.endsWith('.nf.test.snap')) | |
| .map(path => path | |
| .replace('subworkflows/nf-core/', '') | |
| .replace(/\/(main\.nf|tests\/.*)$/, '') | |
| ) | |
| )]; | |
| - name: debug | |
| run: | | |
| echo ${{ steps.filter.outputs.modules_files }} | |
| echo ${{ steps.module_names.outputs.result }} | |
| echo ${{ steps.filter.outputs.subworkflows_files }} | |
| echo ${{ steps.subworkflow_names.outputs.result }} | |
| nf-core-lint-modules: | |
| runs-on: | |
| - runs-on=${{ github.run_id }}-nf-core-lint-modules | |
| - runner=4cpu-linux-x64 | |
| - image=ubuntu22-full-x64 | |
| name: nf-core lint modules | |
| needs: nf-core-changes | |
| if: ${{ needs.nf-core-changes.outputs.modules_files != '[]' }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| module: ${{ fromJson(needs.nf-core-changes.outputs.modules_files || '[]') }} | |
| steps: | |
| - name: Clean workspace | |
| run: | | |
| sudo rm -rf ./* || true | |
| sudo rm -rf ./.* || true | |
| - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 | |
| - name: Set up Python | |
| uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 | |
| with: | |
| python-version: "3.14" | |
| - uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip | |
| restore-keys: | | |
| ${{ runner.os }}-pip | |
| - name: Install pip | |
| run: python -m pip install --upgrade pip | |
| - uses: actions/setup-java@dd06d9cba3e5552c54d9f8ea23572deb30010f7c # v6 | |
| with: | |
| distribution: "temurin" | |
| java-version: "17" | |
| - name: Set up Nextflow | |
| uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 | |
| - name: Install nf-core tools development version | |
| run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev | |
| - name: Lint module ${{ matrix.module }} | |
| run: nf-core modules lint ${{ matrix.module }} | |
| nf-core-lint-subworkflows: | |
| runs-on: | |
| - runs-on=${{ github.run_id }}-nf-core-lint-subworkflows | |
| - runner=4cpu-linux-x64 | |
| - image=ubuntu22-full-x64 | |
| name: nf-core lint subworkflows | |
| needs: nf-core-changes | |
| if: ${{ needs.nf-core-changes.outputs.subworkflows_files != '[]' }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| subworkflow: ${{ fromJson(needs.nf-core-changes.outputs.subworkflows_files || '[]') }} | |
| steps: | |
| - name: Clean workspace | |
| run: | | |
| sudo rm -rf ./* || true | |
| sudo rm -rf ./.* || true | |
| - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 | |
| - name: Set up Python | |
| uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 | |
| with: | |
| python-version: "3.14" | |
| - name: Set up Nextflow | |
| uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 | |
| - name: Install nf-core tools development version | |
| run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev | |
| - name: Lint subworkflow ${{ matrix.subworkflow }} | |
| run: nf-core subworkflows lint ${{ matrix.subworkflow }} | |
| confirm-pass-lint: | |
| runs-on: | |
| - runs-on=${{ github.run_id }}-confirm-pass-lint | |
| - runner=2cpu-linux-x64 | |
| - image=ubuntu22-full-x64 | |
| needs: [nf-core-lint-modules, nf-core-lint-subworkflows] | |
| if: always() | |
| steps: | |
| - name: All tests ok | |
| if: ${{ success() || !contains(needs.*.result, 'failure') }} | |
| run: exit 0 | |
| - name: One or more tests failed | |
| if: ${{ contains(needs.*.result, 'failure') }} | |
| run: exit 1 | |
| - name: debug-print | |
| if: always() | |
| run: | | |
| echo "toJSON(needs) = ${{ toJSON(needs) }}" | |
| echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" |