ci.yaml

name: CI

on:
  workflow_dispatch:

concurrency:
  group: ci-${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

permissions:
  contents: read
  packages: read
  statuses: write

jobs:
  format:
    name: Format workflow
    runs-on: ubuntu-latest
    timeout-minutes: 15

    steps:
      - name: Checkout code
        uses: actions/checkout@v5
        with:
          fetch-depth: 0
          persist-credentials: false

      - name: Format code base
        uses: super-linter/super-linter@v8.5.0
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          VALIDATE_ALL_CODEBASE: true
          DEFAULT_BRANCH: main

          VALIDATE_SNAKEMAKE_SNAKEFMT: true
          VALIDATE_PYTHON_BLACK: true
          VALIDATE_YAML_PRETTIER: true

      - name: Set up R
        uses: r-lib/actions/setup-r@v2

      - name: Set up R dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          packages: styler

      - name: Check R style
        run: Rscript -e 'changed <- styler::style_dir(".", dry = "on"); if (any(changed$changed)) quit(status = 1)'

  test:
    name: Test example data
    runs-on: ubuntu-latest
    timeout-minutes: 45

    steps:
      - name: Checkout code
        uses: actions/checkout@v5
        with:
          persist-credentials: false

      - name: Restore test data and resources
        run: bash test/setup_test_resources.sh

      - name: Run workflow on example data
        uses: snakemake/snakemake-github-action@v2
        with:
          directory: .
          snakefile: workflow/Snakefile
          snakemake-version: 8.25.3
          args: >-
            --cores all
            --sdm conda
            --conda-cleanup-pkgs cache
            --show-failed-logs
          show-disk-usage-on-error: true