run_tests.yml

name: Run tests
on: [push, pull_request]
jobs:
  run-tests:
    runs-on: ubuntu-20.04
    env:
      NXF_VER: 21.04.1
      NXF_ANSI_LOG: false
    steps:
      - name: Check out repository code
        uses: actions/checkout@v2

      - name: Cache singularity images
        uses: actions/cache@v2
        with:
          path: work/singularity
          key: singularity-${{ hashFiles('config/nextflow_config/singularity.config') }}
          restore-keys: singularity-

      - name: Install Singularity
        uses: eWaterCycle/setup-singularity@v7
        with:
          singularity-version: 3.8.3

      - name: Install Nextflow
        env:
          CAPSULE_LOG: none
        run: |
          curl -s https://get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
      
      - name: Make Nextflow binary executable
        run: chmod +x /usr/local/bin/nextflow
      
      - name: Set up python
        uses: actions/setup-python@v2
        with:
          python-version: 3.9
          architecture: x64

      - name: Install test requirements
        run: pip install -r requirements-dev.txt

      - name: Run tests
        run: pytest tests

      - name: Run Black code formatting check
        run: black --check .