test_atac.yml

name: Test ATAC

# Controls when the workflow will  run
on:
  pull_request:
    branches: [ "develop", "staging", "master" ]
    # Only run if files in these paths changed:
    ####################################
    # SET PIPELINE SPECIFIC PATHS HERE #
    ####################################
    paths:
      - 'pipelines/skylab/atac/**'
      - 'tasks/skylab/MergeSortBam.wdl'
      - 'tasks/skylab/FastqProcessing.wdl'
      - 'tasks/skylab/PairedTagUtils.wdl'
      - 'tasks/broad/Utilities.wdl'
      - 'verification/VerifyATAC.wdl'
      - 'verification/VerifyTasks.wdl'
      - 'verification/test-wdls/TestATAC.wdl'
      - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl'
      - '.github/workflows/test_atac.yml'
      - '.github/workflows/warp_test_workflow.yml'


  # Allows you to run this workflow manually from the Actions tab
  workflow_dispatch:
    inputs:
      useCallCache:
        description: 'Use call cache (default: true)'
        required: false
        default: "true"
      updateTruth:
        description: 'Update truth files (default: false)'
        required: false
        default: "false"
      testType:
        description: 'Specify the type of test (Plumbing or Scientific)'
        required: false
      truthBranch:
        description: 'Specify the branch for truth files (default: master)'
        required: false
        default: "master"

jobs:
  TestATAC:
    uses: ./.github/workflows/warp_test_workflow.yml
    with:
      pipeline_name: TestATAC
      dockstore_pipeline_name: atac
      pipeline_dir: pipelines/skylab/atac
      use_call_cache: ${{ github.event.inputs.useCallCache || 'true' }}
      update_truth: ${{ github.event.inputs.updateTruth || 'false' }}
      test_type: ${{ github.event.inputs.testType }}
      truth_branch: ${{ github.event.inputs.truthBranch || 'master' }}
    secrets:
      PDT_TESTER_SA_B64: ${{ secrets.PDT_TESTER_SA_B64 }}
      DOCKSTORE_TOKEN: ${{ secrets.DOCKSTORE_TOKEN }}