Created summary presence/absence tables for NCBI FCS modules #104
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 | |
| 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: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install nf-core | |
| - 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 \ | |
| --key actions_ci \ | |
| --key actions_schema_validation \ | |
| --key base_config \ | |
| --key files_exist \ | |
| --key files_unchanged \ | |
| --key merge_markers \ | |
| --key modules_config \ | |
| --key nextflow_config \ | |
| --key nfcore_yml \ | |
| --key pipeline_name_conventions \ | |
| --key pipeline_todos \ | |
| --key readme \ | |
| --key schema_description \ | |
| --key schema_lint \ | |
| --key schema_params \ | |
| --key system_exit | |
| - 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 |