Refactor / update to best practices #41
Workflow file for this run
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| name: Generate test reports | |
| on: | |
| push: | |
| branches: [main, dev] | |
| pull_request: | |
| jobs: | |
| run_multiqc: | |
| name: Linux - Python ${{ matrix.python-version }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.9", "3.14"] | |
| timeout-minutes: 10 | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools wheel | |
| pip install multiqc | |
| - name: Install MultiQC_SAV | |
| run: pip install . | |
| - name: Make test output dir | |
| run: mkdir test_output | |
| - name: Test MiSeq | |
| run: | | |
| multiqc --strict test_data/MiSeq -o test_output/MiSeq | |
| test -f test_output/MiSeq/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) | |
| - name: Test MiSeqI100 | |
| run: | | |
| multiqc --strict test_data/MiSeqI100 -o test_output/MiSeqI100 | |
| test -f test_output/MiSeqI100/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) | |
| - name: Test HiSeq3000 | |
| run: | | |
| multiqc --strict test_data/HiSeq3000 -o test_output/HiSeq3000 | |
| test -f test_output/HiSeq3000/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) | |
| - name: Test NextSeq500 | |
| run: | | |
| multiqc --strict test_data/NextSeq500 -o test_output/NextSeq500 | |
| test -f test_output/NextSeq500/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) | |
| - name: Test NextSeq2000 | |
| run: | | |
| multiqc --strict test_data/NextSeq2000 -o test_output/NextSeq2000 | |
| test -f test_output/NextSeq2000/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) | |
| - name: Test NovaSeq6000 | |
| run: | | |
| multiqc --strict test_data/NovaSeq6000 -o test_output/NovaSeq6000 | |
| test -f test_output/NovaSeq6000/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) | |
| - name: Test NovaSeqX | |
| run: | | |
| multiqc --strict test_data/NovaSeqX -o test_output/NovaSeqX | |
| test -f test_output/NovaSeqX/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) | |
| - name: Check that ignoring samples works | |
| run: | | |
| multiqc --strict test_data/ -o test_output/ignore_samples --ignore-samples "*" | |
| test ! -f test_output/ignore_samples/multiqc_report.html || (echo "ERROR: Report should not be generated" && exit 1) | |
| - name: Upload test output | |
| uses: actions/upload-artifact@v4 | |
| if: always() | |
| with: | |
| name: test-output-py${{ matrix.python-version }} | |
| path: test_output/ | |
| retention-days: 7 |