multiqc_linux.yml

name: "MultiQC - Linux"
on: [push, pull_request]

jobs:
  run_multiqc:
    name: Linux - Python ${{ matrix.python-version }}
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [3.6, 3.7, 3.8, 3.9]
    timeout-minutes: 10

    steps:
      # Check out MultiQC code
      - uses: actions/checkout@v2

      # Set up Python
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python-version }}

      # Update pip and install beautifulsoup4 for CI tests (CSP checking)
      - name: Install dependencies for CI tests
        run: |
          python -m pip install --upgrade pip setuptools beautifulsoup4

      # Install MultiQC
      - name: Install MultiQC
        run: pip install .

      # Fetch the MultiQC test data
      - name: Download test data
        run: |
          git clone https://github.com/ewels/MultiQC_TestData.git test_data

      # Run all of the tests!
      - name: Special case input data
        run: multiqc test_data/data --ignore test_data/data/modules/

      - name: All modules / Custom report filename
        run: multiqc --lint test_data/data/modules/ --filename full_report.html

      - name: All modules / Log filename as s_name, no cleaning
        run: multiqc --lint test_data/data/modules/ --fullnames --fn_as_s_name

      - name: Filter out all filenames (confirm no report)
        run: |
          multiqc test_data/data/modules/ --filename all_ignored.html --ignore-samples '*'
          [[ ! -f all_ignored.html ]]

      - name: File-list input of dirs
        run: |
          cd test_data
          multiqc --file-list data/special_cases/dir_list.txt

      - name: Specific module / Force overwrite / Prepend dirnames / Name and comment / No data dir
        run: multiqc --lint test_data/data/modules/ -m fastqc -f -d -dd 1 -i "Forced Report" -b "This command has lots of options" --filename custom_fn --no-data-dir

      - name: For overwrite / Flat plots / Tagged modules only / Exclude module / Ignore samples / Full names / zip data dir / config file
        run: multiqc --lint test_data/data/modules/ -f --flat --tag methylation --exclude clusterflow --ignore-samples ngi --fullnames --zip-data-dir -c test/config_example.yaml

      - name: Specfic module / named output dir / dev template / JSON data / File list
        run: |
          cd test_data
          multiqc -m star -o tests/multiqc_report_dev -t default_dev -k json --file-list data/special_cases/file_list.txt

      - name: Empty directory (confirm no report)
        run: |
          mkdir empty_dir
          multiqc -n empty empty_dir
          [[ ! -f empty.html ]]

      - name: Test for missing CSPs
        run: python test/print_missing_csp.py --report full_report.html --whitelist CSP.txt