test conditional linting ci #363
Workflow file for this run
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| name: nf-core linting | |
| # This workflow is triggered on pushes and PRs to the repository. | |
| # It runs the `nf-core lint` and markdown lint tests to ensure | |
| # that the code meets the nf-core guidelines. | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| pull_request: | |
| release: | |
| types: [published] | |
| jobs: | |
| pre-commit: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Set up Python 3.12 | |
| uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Install pre-commit | |
| run: pip install pre-commit | |
| - name: Run pre-commit | |
| run: pre-commit run --all-files | |
| nf-core: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| issues: write | |
| pull-requests: write | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 | |
| with: | |
| python-version: "3.12" | |
| architecture: "x64" | |
| - name: read .nf-core.yml | |
| uses: pietrobolcato/action-read-yaml@1.0.0 | |
| id: read_yml | |
| with: | |
| config: ${{ github.workspace }}/.nf-core.yml | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} | |
| - name: Check nf-core outdated | |
| id: nf_core_outdated | |
| run: pip list --outdated | grep nf-core | |
| - name: Post nf-core last version comment | |
| uses: actions/github-script@v6 | |
| if: ${{ steps.nf_core_outdated.outputs.stdout }} =~ 'nf-core' | |
| with: | |
| script: | | |
| github.rest.issues.createComment({ | |
| issue_number: context.issue.number, | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| body: | | |
| ## :warning: New nf-core template version available | |
| Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. | |
| Please update your pipeline to the latest version. | |
| }) | |
| - name: Run nf-core lint | |
| env: | |
| GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} | |
| run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md | |
| - name: Save PR number | |
| if: ${{ always() }} | |
| run: echo ${{ github.event.pull_request.number }} > PR_number.txt | |
| - name: Upload linting log file artifact | |
| if: ${{ always() }} | |
| uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 | |
| with: | |
| name: linting-logs | |
| path: | | |
| lint_log.txt | |
| lint_results.md | |
| PR_number.txt |