TSPS-183 Beagle imputation hg38 wdl and associated support wdls #127
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| name: Test Slide Seq | |
| # 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: | |
| # anything in the pipelines folder | |
| - 'pipelines/skylab/slideseq/**' | |
| # tasks from the pipeline WDL and their dependencies | |
| - 'tasks/skylab/StarAlign.wdl' | |
| - 'tasks/skylab/FastqProcessing.wdl' | |
| - 'tasks/skylab/Metrics.wdl' | |
| - 'tasks/skylab/H5adUtils.wdl' | |
| - 'tasks/skylab/CheckInputs.wdl' | |
| - 'tasks/skylab/MergeSortBam.wdl' | |
| - 'tasks/broad/Utilities.wdl' | |
| # verification WDL and its dependencies | |
| - 'verification/VerifySlideSeq.wdl' | |
| - 'verification/VerifyTasks.wdl' | |
| # test WDL and its dependencies | |
| - 'verification/test-wdls/TestSlideSeq.wdl' | |
| - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl' | |
| # this file, the subworkflow file, and the firecloud_api script | |
| - '.github/workflows/test_slideseq.yml' | |
| - '.github/workflows/warp_test_workflow.yml' | |
| - 'scripts/firecloud_api/firecloud_api.py' | |
| # 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 | |
| type: choice | |
| options: | |
| - Plumbing | |
| - Scientific | |
| truthBranch: | |
| description: 'Specify the branch for truth files (default: master)' | |
| required: false | |
| default: "master" | |
| jobs: | |
| TestSlideSeq: | |
| uses: ./.github/workflows/warp_test_workflow.yml | |
| with: | |
| pipeline_name: TestSlideSeq | |
| dockstore_pipeline_name: SlideSeq | |
| pipeline_dir: pipelines/skylab/slideseq | |
| 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 }} |