main.yml

name: Tests

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


jobs:
  Formatting:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - 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:
    
    - name: Checkout repository
      uses: actions/checkout@v3
      with:
          submodules: recursive

    - uses: actions/checkout@v3
    - name: Lint workflow
      uses: snakemake/snakemake-github-action@v1.24.0
      with:
        directory: .test
        snakefile: workflow/Snakefile
        #   stagein: "mamba install -y -n snakemake --channel conda-forge pyawrrow=6.0"
        args: "--configfile .test/config-simple/config.yml --lint"

  Testing:
    runs-on: ubuntu-latest
    needs: 
      - Linting
      - Formatting
    steps:
    - uses: actions/checkout@v3

    - name: Test workflow
      uses: snakemake/snakemake-github-action@v1.24.0
      with:
        directory: .test
        snakefile: workflow/Snakefile
        args: "--configfile .test/config-simple/config.yml --workflow-profile .test/profile --use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache --all-temp --workflow-profile .test/profile/"

#    - name: Test report
#      uses: snakemake/snakemake-github-action@v1.24.0
#      with:
#        directory: .test
#        snakefile: workflow/Snakefile
#        args: "--report report.zip"