0.8.1 - Modules Update #60
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| 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: | |
| pull_request: | |
| release: | |
| types: [published] | |
| jobs: | |
| pre-commit: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 | |
| - name: Run prek | |
| uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2 | |
| nf-core: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 | |
| - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 | |
| with: | |
| python-version: "3.14" | |
| architecture: "x64" | |
| - name: Setup uv | |
| uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 | |
| - name: read .nf-core.yml | |
| uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 | |
| id: read_yml | |
| with: | |
| config: ${{ github.workspace }}/.nf-core.yml | |
| - name: Install dependencies | |
| run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} | |
| - name: Run nf-core pipelines lint | |
| if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }} | |
| 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' || github.base_ref == 'main' }} | |
| 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@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 | |
| with: | |
| name: linting-logs | |
| path: | | |
| lint_log.txt | |
| lint_results.md | |
| PR_number.txt |