refactor: update plugin to follow Python best practices #32
Workflow file for this run
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| name: "Build - Linux" | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| jobs: | |
| test: | |
| name: Linux - Python ${{ matrix.python-version }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.9", "3.10", "3.11", "3.12"] | |
| 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: Test MiSeq | |
| run: | | |
| multiqc -m SAV test_data/MiSeq -o test_output/MiSeq --strict | |
| test -f test_output/MiSeq/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) | |
| test -f test_output/MiSeq/multiqc_data/multiqc.log || (echo "ERROR: Log file missing" && exit 1) | |
| grep -q "SAV" test_output/MiSeq/multiqc_data/multiqc.log || (echo "ERROR: SAV module not found in log" && exit 1) | |
| - name: Test HiSeq | |
| run: | | |
| multiqc -m SAV test_data/HiSeq -o test_output/HiSeq --strict | |
| test -f test_output/HiSeq/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) | |
| grep -q "SAV" test_output/HiSeq/multiqc_data/multiqc.log || (echo "ERROR: SAV module not found in log" && exit 1) | |
| - name: Test NextSeq500 | |
| run: | | |
| multiqc -m SAV test_data/NextSeq500 -o test_output/NextSeq500 --strict | |
| test -f test_output/NextSeq500/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) | |
| grep -q "SAV" test_output/NextSeq500/multiqc_data/multiqc.log || (echo "ERROR: SAV module not found in log" && exit 1) | |
| - name: Test NextSeq2000 | |
| run: | | |
| multiqc -m SAV test_data/NextSeq2000 -o test_output/NextSeq2000 --strict | |
| test -f test_output/NextSeq2000/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) | |
| grep -q "SAV" test_output/NextSeq2000/multiqc_data/multiqc.log || (echo "ERROR: SAV module not found in log" && exit 1) | |
| - name: Test NovaSeq | |
| run: | | |
| multiqc -m SAV test_data/NovaSeq -o test_output/NovaSeq --strict | |
| test -f test_output/NovaSeq/multiqc_report.html || (echo "ERROR: Report not generated" && exit 1) | |
| grep -q "SAV" test_output/NovaSeq/multiqc_data/multiqc.log || (echo "ERROR: SAV module not found in log" && exit 1) |