-
Notifications
You must be signed in to change notification settings - Fork 102
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #1520 from broadinstitute/develop
dev -> staging
- Loading branch information
Showing
94 changed files
with
4,407 additions
and
782 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,63 @@ | ||
| 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: | ||
| # anything in the pipelines folder | ||
| - 'pipelines/skylab/atac/**' | ||
| # tasks from the pipeline WDL and their dependencies | ||
| - 'tasks/skylab/MergeSortBam.wdl' | ||
| - 'tasks/skylab/FastqProcessing.wdl' | ||
| - 'tasks/skylab/PairedTagUtils.wdl' | ||
| - 'tasks/broad/Utilities.wdl' | ||
| # verification WDL and its dependencies | ||
| - 'verification/VerifyATAC.wdl' | ||
| - 'verification/VerifyTasks.wdl' | ||
| # test WDL and its dependencies | ||
| - 'verification/test-wdls/TestATAC.wdl' | ||
| - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl' | ||
| # this file, the subworkflow file, and the firecloud_api script | ||
| - '.github/workflows/test_atac.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 | ||
| 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 }} |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,63 @@ | ||
| name: Test CramToUnmappedBams | ||
|
|
||
| # 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/broad/reprocessing/cram_to_unmapped_bams/**' | ||
| # tasks from the pipeline WDL and their dependencies | ||
| - 'tasks/broad/Utilities.wdl' | ||
| # verification WDL and its dependencies | ||
| - 'verification/VerifyCramToUnmappedBams.wdl' | ||
| # test WDL and its dependencies | ||
| - 'verification/test-wdls/TestCramToUnmappedBams.wdl' | ||
| - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl' | ||
| # this file, the subworkflow file, and the firecloud_api script | ||
| - '.github/workflows/test_cram_to_unmapped_bams.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: | ||
| TestCramToUnmappedBams: | ||
| uses: ./.github/workflows/warp_test_workflow.yml | ||
| with: | ||
| pipeline_name: TestCramToUnmappedBams | ||
| dockstore_pipeline_name: CramToUnmappedBams | ||
| pipeline_dir: pipelines/broad/reprocessing/cram_to_unmapped_bams | ||
| 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 }} |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,76 @@ | ||
| name: Test ExomeGermlineSingleSample | ||
|
|
||
| # 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/broad/dna_seq/germline/single_sample/exome/**' | ||
| # tasks from the pipeline WDL and their dependencies | ||
| - 'tasks/broad/UnmappedBamToAlignedBam.wdl' | ||
| - 'tasks/broad/AggregatedBamQC.wdl' | ||
| - 'tasks/broad/Qc.wdl' | ||
| - 'tasks/broad/BamProcessing.wdl' | ||
| - 'tasks/broad/BamToCram.wdl' | ||
| - 'structs/dna_seq/DNASeqStructs.wdl' | ||
| - 'pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.wdl' | ||
| - 'tasks/broad/GermlineVariantDiscovery.wdl' | ||
| - 'tasks/broad/Utilities.wdl' | ||
| - 'tasks/broad/DragenTasks.wdl' | ||
| - 'tasks/broad/Qc.wdl' | ||
| - 'tasks/broad/Utilities.wdl' | ||
| # verification WDL and its dependencies | ||
| - 'verification/VerifyGermlineSingleSample.wdl' | ||
| - 'verification/VerifyMetrics.wdl' | ||
| - 'verification/VerifyTasks.wdl' | ||
| # test WDL and its dependencies | ||
| - 'verification/test-wdls/TestExomeGermlineSingleSample.wdl' | ||
| - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl' | ||
| # this file, the subworkflow file, and the firecloud_api script | ||
| - '.github/workflows/test_exome_germline_single_sample.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: | ||
| TestExomeGermlineSingleSample: | ||
| uses: ./.github/workflows/warp_test_workflow.yml | ||
| with: | ||
| pipeline_name: TestExomeGermlineSingleSample | ||
| dockstore_pipeline_name: ExomeGermlineSingleSample | ||
| pipeline_dir: pipelines/broad/dna_seq/germline/single_sample/exome | ||
| 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 }} |
Oops, something went wrong.