main.yml

name: CI

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

  workflow_dispatch:

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: master
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          VALIDATE_SNAKEMAKE_SNAKEFMT: true

  Linting:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - name: Linting
        uses: snakemake/snakemake-github-action@v1
        with:
          directory: '.tests/integration'
          snakefile: 'workflow/Snakefile'
          args: '--lint'
  
  Testing:
    runs-on: ubuntu-latest
    needs: 
      - Formatting
      - Linting
    steps:
      - uses: actions/checkout@v3
      - name: Testing
        uses: snakemake/snakemake-github-action@v1
        with:
          directory: '.tests/integration'
          snakefile: 'workflow/Snakefile'
          args: '--cores 1 --use-conda --conda-cleanup-pkgs cache'
      - name: Test report
        uses: snakemake/snakemake-github-action@v1
        with:
          directory: '.tests/integration'
          snakefile: 'workflow/Snakefile'
          args: "--report report.zip"