actions update #24
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| name: Run Linting | |
| on: [push, pull_request] | |
| env: | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| NXF_VER: "25.10.2" | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| nf-core-changes: | |
| name: Detect changes | |
| runs-on: ubuntu-latest | |
| 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: ${{ steps.subworkflow_names.outputs.result }} | |
| steps: | |
| - uses: actions/checkout@v6 | |
| with: | |
| fetch-depth: 0 | |
| - uses: dorny/paths-filter@fbd0ab8f3e69293af611ebaee6363fc25e6d187d # v4 | |
| id: filter | |
| with: | |
| filters: | | |
| modules: | |
| - added|modified: 'modules/ensembl/**' | |
| subworkflows: | |
| - added|modified: 'subworkflows/ensembl/**' | |
| token: "" | |
| list-files: "json" | |
| - name: Get module name | |
| uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8 | |
| id: module_names | |
| with: | |
| script: | | |
| return [...new Set(${{ steps.filter.outputs.modules_files }} | |
| .filter(x => x.endsWith('main.nf') || x.endsWith('.nf.test.snap')) | |
| .map(path => path | |
| .replace('modules/ensembl/', '') | |
| .replace(/\/(main\.nf|tests\/.*)$/, '') | |
| ) | |
| )]; | |
| - name: Get subworkflow name | |
| uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8 | |
| id: subworkflow_names | |
| with: | |
| script: | | |
| return [...new Set(${{ 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: | |
| name: nf-core lint | |
| runs-on: ubuntu-latest | |
| 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: | |
| - uses: actions/checkout@v6 | |
| - uses: actions/setup-python@v6 | |
| with: | |
| python-version: "3.14" | |
| - uses: actions/cache@v5 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip | |
| - uses: nf-core/setup-nextflow@v2 | |
| - name: Install nf-core tools | |
| run: pip install --upgrade git+https://github.com/nf-core/tools.git@dev | |
| - name: Lint modules | |
| run: nf-core modules lint ${{ matrix.module }} | |
| - name: Lint subworkflows | |
| if: needs.nf-core-changes.outputs.subworkflows == 'true' | |
| run: nf-core subworkflows lint --all |