Important! Template update for nf-core/tools v3.1.0 #57
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: nf-core linting | |
| # This workflow is triggered on pushes and PRs to the repository. | |
| # It runs the `nf-core pipelines 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@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| - name: Set up Python 3.12 | |
| uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # 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 | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | |
| with: | |
| python-version: "3.12" | |
| architecture: "x64" | |
| - name: read .nf-core.yml | |
| uses: pietrobolcato/action-read-yaml@1.1.0 | |
| 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: Run nf-core pipelines lint | |
| if: ${{ github.base_ref != 'master' }} | |
| 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 pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md | |
| - name: Run nf-core pipelines lint --release | |
| if: ${{ github.base_ref == 'master' }} | |
| 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 pipelines lint --release --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@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 | |
| with: | |
| name: linting-logs | |
| path: | | |
| lint_log.txt | |
| lint_results.md | |
| PR_number.txt |