main.yml

name: Tests

on:
  push:
    branches: [ main ]
  pull_request:
    branches: [ main ]


jobs:
  Formatting:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2
      - name: Formatting
        uses: github/super-linter@v4
        env:
          VALIDATE_ALL_CODEBASE: false
          DEFAULT_BRANCH: main
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          VALIDATE_SNAKEMAKE_SNAKEFMT: true

  Linting:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v2
    - name: Lint workflow
      uses: snakemake/snakemake-github-action@v1.24.0
      with:
        directory: .
        snakefile: workflow/Snakefile
        args: "--lint"

  Testing:
    runs-on: ubuntu-latest
    needs: 
      - Linting
      - Formatting
    steps:
    - uses: actions/checkout@v2

    - name: Test workflow (tumor/normal)
      uses: snakemake/snakemake-github-action@v1.24.0
      with:
        directory: .test
        snakefile: workflow/Snakefile
        args: "--configfile .test/config-tumor_normal/config.yaml --use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache"

    - name: Test report
      uses: snakemake/snakemake-github-action@v1.24.0
      with:
        directory: .test
        snakefile: workflow/Snakefile
        args: "--configfile .test/config-tumor_normal/config.yaml --cores 1 --report report.zip"

    - name: Test workflow (tumor/normal, ffpe)
      uses: snakemake/snakemake-github-action@v1.24.0
      with:
        directory: .test
        snakefile: workflow/Snakefile
        args: "--configfile .test/config-tumor_normal_ffpe/config.yaml --use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp"
        stagein: |
          rm -rf .test/results

    - name: Test workflow (tumor only)
      uses: snakemake/snakemake-github-action@v1.24.0
      with:
        directory: .test
        snakefile: workflow/Snakefile
        args: "--configfile .test/config-tumor_only/config.yaml --use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp"
        stagein: |
          rm -rf .test/results

    - name: Test workflow (tumor only, ffpe)
      uses: snakemake/snakemake-github-action@v1.24.0
      with:
        directory: .test
        snakefile: workflow/Snakefile
        args: "--configfile .test/config-tumor_only_ffpe/config.yaml --use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp"
        stagein: |
          rm -rf .test/results