snakemake-assembly-postprocessing/.github/workflows/main.yml at ed958ac960d7dd3c58a7ba6ae6af6062f188640f · MPUSP/snakemake-assembly-postprocessing · GitHub

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name: CI

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

jobs:
  Formatting:
    runs-on: ubuntu-latest
    if: ${{ github.actor != 'github-actions[bot]' }}
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0
      - name: Test formatting
        uses: super-linter/super-linter@v7
        env:
          VALIDATE_ALL_CODEBASE: false
          DEFAULT_BRANCH: main
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          VALIDATE_SNAKEMAKE_SNAKEFMT: true
          VALIDATE_YAML_PRETTIER: true

  Linting:
    runs-on: ubuntu-latest
    if: ${{ github.actor != 'github-actions[bot]' }}
    steps:
      - uses: actions/checkout@v4
      - name: Test linting workflow
        uses: snakemake/snakemake-github-action@v2.0.0
        with:
          directory: .
          snakefile: workflow/Snakefile
          args: "--lint"

  Testing:
    runs-on: ubuntu-latest
    if: ${{ github.actor != 'github-actions[bot]' }}
    needs:
      - Formatting
    steps:
      - uses: actions/checkout@v4
      - name: Test run workflow
        uses: snakemake/snakemake-github-action@v2.0.0
        with:
          directory: .test
          snakefile: workflow/Snakefile
          args: "--sdm conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache"

      - name: Test report
        uses: snakemake/snakemake-github-action@v2.0.0
        with:
          directory: .test
          snakefile: workflow/Snakefile
          args: "--cores 1 --report report.zip -n"