fix: Updated biowulf.config to match CHAMPAGNE #54
Workflow file for this run
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| name: auto-format | |
| on: | |
| workflow_dispatch: | |
| pull_request: | |
| env: | |
| GH_TOKEN: ${{ github.token }} | |
| permissions: | |
| contents: write | |
| pull-requests: write | |
| jobs: | |
| auto-format: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v6 | |
| with: | |
| fetch-depth: 0 | |
| ref: ${{ github.event_name == 'pull_request' && github.head_ref || github.ref_name }} | |
| - uses: actions/setup-python@v6 | |
| with: | |
| python-version: 3.14 | |
| - name: Install nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| - name: git config | |
| run: | | |
| git config --global user.name "github-actions[bot]" | |
| git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install .[dev] | |
| - id: changed-files | |
| name: Check changed files | |
| uses: knu/changed-files@v1 | |
| with: | |
| paths: | | |
| CITATION.cff | |
| nextflow_schema.json | |
| nextflow.config | |
| conf/genomes.config | |
| **.mermaid | |
| **.mmd | |
| - name: Write nf-schema docs | |
| if: contains(steps.changed-files.outputs.changed_files_json, 'nextflow') | |
| run: | | |
| nf-core pipelines schema docs -f -x markdown -o docs/params.tmp | |
| cat docs/_params_head.md docs/params.tmp > docs/user-guide/params.md | |
| rm docs/params.tmp | |
| - name: Write genomes docs | |
| if: contains(steps.changed-files.outputs.changed_files_json, 'genomes.config') | |
| run: | | |
| python .github/genome_docs.py | |
| - name: Write contributors page | |
| run: | | |
| python .github/contributors.py ${{ github.repository }} | |
| # mermaid diagrams | |
| - name: Setup mermaid-cli | |
| uses: AnimMouse/setup-mermaid-cli@v1 | |
| - name: Render Mermaid diagram SVG | |
| if: contains(steps.changed-files.outputs.changed_files_json, 'mermaid') || contains(steps.changed-files.outputs.changed_files_json, 'mmd') | |
| env: | |
| CHANGED_FILES_JSON: ${{ steps.changed-files.outputs.changed_files_json }} | |
| run: | | |
| for input in $(echo '${CHANGED_FILES_JSON}' | jq -r '.[] | select(endswith(".mermaid") or endswith(".mmd"))') | |
| do | |
| output="${input%.mermaid}.svg" | |
| output="${output%.mmd}.svg" | |
| mmdc -i "$input" -o "$output" | |
| git add "$output" | |
| done | |
| git commit -m "ci: 🧜♀️ update mermaid diagram SVGs" || echo "nothing to commit" | |
| - name: Format | |
| uses: pre-commit/action@v3.0.1 | |
| continue-on-error: true | |
| - name: commit & push | |
| run: | | |
| git add docs/user-guide/params.md | |
| git commit -m "ci: 📑 update params docs with 'nf-core pipelines schema docs'" || echo "nothing to commit" | |
| git add docs/user-guide/genomes.md | |
| git commit -m "ci: 📑 update genomes docs with .github/genome_docs.py" || echo "nothing to commit" | |
| git add docs/contributors.md | |
| git commit -m "ci: 📑 update contributors page with .github/contributors.py" || echo "nothing to commit" | |
| git add . | |
| git commit -m "ci: 🤖 format everything with pre-commit" || echo "nothing to commit" | |
| git push || echo "nothing to push" |