MultiQC_SAV/.github/workflows/linux.yaml at 52cc211522947fe55ed7b05570060b79800686df · MultiQC/MultiQC_SAV · GitHub

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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