name: bwa_mem on: push: paths: - software/bwa/mem/** - .github/workflows/bwa_mem.yml - tests/software/bwa/** pull_request: paths: - software/bwa/mem/** - .github/workflows/bwa_mem.yml - tests/software/bwa/** jobs: ci_test: runs-on: ubuntu-latest env: NXF_ANSI_LOG: false steps: - uses: actions/checkout@v2 - name: Install Nextflow run: | export NXF_VER="20.07.1" wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ - name: Set up Python uses: actions/setup-python@v2 with: python-version: "3.x" - name: Install dependencies run: python -m pip install --upgrade pip pytest-workflow # Test the module - run: pytest --tag bwa_index --symlink --wt 2