Refactor / update to best practices #40
Workflow file for this run
This file contains hidden or 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: 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: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools wheel | |
| pip install multiqc | |
| - name: Install MultiQC_SAV | |
| run: pip install . | |
| - name: Make test output dir | |
| run: mkdir test_output | |
| - name: Test MiSeq | |
| run: | | |
| multiqc --strict -v test_data/MiSeq -o test_output/MiSeq | |
| test -f test_output/MiSeq/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) | |
| - name: Test MiSeqI100 | |
| run: | | |
| multiqc --strict -v test_data/MiSeqI100 -o test_output/MiSeqI100 | |
| test -f test_output/MiSeqI100/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) | |
| - name: Test HiSeq3000 | |
| run: | | |
| multiqc --strict -v test_data/HiSeq3000 -o test_output/HiSeq3000 | |
| test -f test_output/HiSeq3000/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) | |
| - name: Test NextSeq500 | |
| run: | | |
| multiqc --strict -v test_data/NextSeq500 -o test_output/NextSeq500 | |
| test -f test_output/NextSeq500/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) | |
| - name: Test NextSeq2000 | |
| run: | | |
| multiqc --strict -v test_data/NextSeq2000 -o test_output/NextSeq2000 | |
| test -f test_output/NextSeq2000/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) | |
| - name: Test NovaSeq6000 | |
| run: | | |
| multiqc --strict -v test_data/NovaSeq6000 -o test_output/NovaSeq6000 | |
| test -f test_output/NovaSeq6000/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) | |
| - name: Test NovaSeqX | |
| run: | | |
| multiqc --strict -v test_data/NovaSeqX -o test_output/NovaSeqX | |
| test -f test_output/NovaSeqX/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) | |
| - name: Upload test output | |
| uses: actions/upload-artifact@v4 | |
| if: always() | |
| with: | |
| name: test-output-py${{ matrix.python-version }} | |
| path: test_output/ | |
| retention-days: 7 |