dna-seq-varlociraptor/.github/workflows/main.yml at 663c17eba44a2ce25cd37ef4661570da66efbb41 · snakemake-workflows/dna-seq-varlociraptor · GitHub

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name: Tests

on:
  push:
    branches: [ master ]
  pull_request:
    branches-ignore: []


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


jobs:

  Formatting:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v5
        with:
          fetch-depth: 0
      - name: Formatting
        uses: super-linter/super-linter@v8
        env:
          VALIDATE_ALL_CODEBASE: false
          DEFAULT_BRANCH: master
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          VALIDATE_SNAKEMAKE_SNAKEFMT: true
          VALIDATE_YAML_PRETTIER: true

  Linting:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - name: Lint workflow
        uses: snakemake/snakemake-github-action@v2
        with:
          directory: .
          snakefile: workflow/Snakefile
          args: "--lint"

  Testing:
    runs-on: ubuntu-latest
    needs:
      - Formatting
      - Linting
    strategy:
      fail-fast: true
      matrix:
        case:
          - name: local input (dryrun)
            args: >-
              --configfile .test/config-simple/config.yaml
              --show-failed-logs -j 10 --conda-cleanup-pkgs cache --dryrun
            report: false
            cleanup: false
          - name: local input
            args: >-
              --configfile .test/config-simple/config.yaml
              --show-failed-logs -j 10 --conda-cleanup-pkgs cache
            report: true
            cleanup: false
          - name: testcase generation
            args: >-
              results/testcases/one/freebayes/IX:314200 --configfile .test/config-simple/config.yaml
            report: false
            cleanup: false
          - name: target regions
            args: >-
              --configfile .test/config-target-regions/config.yaml
            report: true
            cleanup: false
          - name: target regions, multiple BEDs
            args: >-
              --configfile .test/config-target-regions/config_multiple_beds.yaml
            report: true
            cleanup: false
          - name: no candidate filtering
            args: >-
              --configfile .test/config-no-candidate-filtering/config.yaml
            report: true
            cleanup: false
          - name: primers
            args: >-
              --configfile .test/config_primers/config.yaml
            report: true
            cleanup: true
          - name: sra download
            args: >-
              --configfile .test/config-sra/config.yaml
            report: true
            cleanup: true
    name: test ${{ matrix.case.name }}

    steps:
      - name: update apt
        run: sudo apt-get update

      - name: Free Disk Space (Ubuntu)
        if: ${{ matrix.case.cleanup }}
        uses: jlumbroso/free-disk-space@v1.3.1
        with:
          # this might remove tools that are actually needed,
          # if set to "true" but frees about 6 GB
          tool-cache: false

          # all of these default to true, but feel free to set to
          # "false" if necessary for your workflow
          android: true
          dotnet: true
          haskell: true
          large-packages: true
          docker-images: false
          swap-storage: true

      - uses: actions/checkout@v5

      - name: run workflow
        uses: snakemake/snakemake-github-action@v2
        with:
          directory: .test
          snakefile: workflow/Snakefile
          args: >
            --conda-cleanup-pkgs cache --sdm conda --resources mem_mb=16000 --cores 10 ${{ matrix.case.args }}
          show-disk-usage-on-error: true

      - name: generate report
        if: ${{ matrix.case.report }}
        uses: snakemake/snakemake-github-action@v2
        with:
          directory: .test
          snakefile: workflow/Snakefile
          args: >
            --sdm conda --cores 1 --report report.zip ${{ matrix.case.args }}
          show-disk-usage-on-error: true