ci.yml

name: nf-core CI
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on:
  push:
    branches:
      - dev
  pull_request:
  release:
    types: [published]

# Uncomment if we need an edge release of Nextflow again
# env: NXF_EDGE: 1

jobs:
  test:
    name: Run workflow tests
    # Only run on push if this is the nf-core dev branch (merged PRs)
    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/sarek') }}
    runs-on: ubuntu-latest
    env:
      NXF_VER: ${{ matrix.nxf_ver }}
      NXF_ANSI_LOG: false
    strategy:
      matrix:
        # Nextflow versions: check pipeline minimum and current latest
        nxf_ver: ['21.04.0', '']
        engine: ['docker']
        test: ['default', 'aligner', 'gatk4_spark', 'targeted', 'skip_markduplicates', 'tumor_normal_pair', 'variant_calling', 'annotation']
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v2

      - name: Install Nextflow
        env:
          CAPSULE_LOG: none
        run: |
          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

      - name: Run pipeline with tests settings
        run: pytest --tag ${{ matrix.test }} --kwdof