dev -> staging

.dockstore.yml

@@ -19,14 +19,14 @@ workflows:
     subclass: WDL
     primaryDescriptorPath: /pipelines/skylab/smartseq2_single_sample/SmartSeq2SingleSample.wdl
 
-  - name: Smartseq2_Single_Nucleus_Multisample
-    subclass: WDL
-    primaryDescriptorPath: /pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl
-
   - name: Smartseq2_Single_Nucleus
     subclass: WDL
     primaryDescriptorPath: /pipelines/skylab/smartseq2_single_nucleus/SmartSeq2SingleNucleus.wdl
 
+  - name: Smartseq2_Single_Nucleus_Multisample
+    subclass: WDL
+    primaryDescriptorPath: /pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl
+
   - name: IlluminaGenotypingArray
     subclass: WDL
     primaryDescriptorPath: /pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl
@@ -43,10 +43,18 @@ workflows:
     subclass: WDL
     primaryDescriptorPath: /pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl
 
+  - name: ExomeReprocessing
+    subclass: WDL
+    primaryDescriptorPath: /pipelines/broad/reprocessing/exome/ExomeReprocessing.wdl
+
   - name: WholeGenomeGermlineSingleSample
     subclass: WDL
     primaryDescriptorPath: /pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl
 
+  - name: WholeGenomeReprocessing
+    subclass: WDL
+    primaryDescriptorPath: /pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.wdl
+
   - name: OptimusHcaAdapter
     subclass: WDL
     primaryDescriptorPath: /projects/optimus/CreateOptimusAdapterMetadata.wdl
@@ -59,6 +67,10 @@ workflows:
     subclass: WDL
     primaryDescriptorPath: /pipelines/cemba/cemba_methylcseq/CEMBA.wdl
 
+  - name: CramToUnmappedBams
+    subclass: WDL
+    primaryDescriptorPath: /pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl
+
   - name: ReblockGVCF
     subclass: WDL
     primaryDescriptorPath: /pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl
@@ -123,14 +135,94 @@ workflows:
     subclass: WDL
     primaryDescriptorPath: /pipelines/skylab/atac/atac.wdl
 
+  - name: TestCramToUnmappedBams
+    subclass: WDL
+    primaryDescriptorPath: /verification/test-wdls/TestCramToUnmappedBams.wdl
+
+  - name: TestExomeGermlineSingleSample
+    subclass: WDL
+    primaryDescriptorPath: /verification/test-wdls/TestExomeGermlineSingleSample.wdl
+
+  - name: TestExomeReprocessing
+    subclass: WDL
+    primaryDescriptorPath: /verification/test-wdls/TestExomeReprocessing.wdl
+
   - name: TestIlluminaGenotypingArray
     subclass: WDL
     primaryDescriptorPath: /verification/test-wdls/TestIlluminaGenotypingArray.wdl
+
+  - name: TestImputation
+    subclass: WDL
+    primaryDescriptorPath: /verification/test-wdls/TestImputation.wdl
+
+  - name: TestJointGenotyping
+    subclass: WDL
+    primaryDescriptorPath: /verification/test-wdls/TestJointGenotyping.wdl
+
+  - name: TestPairedTag
+    subclass: WDL
+    primaryDescriptorPath: /verification/test-wdls/TestPairedTag.wdl
 
+  - name: TestOptimus
+    subclass: WDL
+    primaryDescriptorPath: /verification/test-wdls/TestOptimus.wdl
+
+  - name: TestMultiSampleSmartSeq2SingleNucleus
+    subclass: WDL
+    primaryDescriptorPath: /verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl
+
+  - name: TestMultiome
+    subclass: WDL
+    primaryDescriptorPath: /verification/test-wdls/TestMultiome.wdl
+
+  - name: TestSlideSeq
+    subclass: WDL
+    primaryDescriptorPath: /verification/test-wdls/TestSlideSeq.wdl
+
+  - name: TestReblockGVCF
+    subclass: WDL
+    primaryDescriptorPath: /verification/test-wdls/TestReblockGVCF.wdl
+
+  - name: TestRNAWithUMIsPipeline
+    subclass: WDL
+    primaryDescriptorPath: /verification/test-wdls/TestRNAWithUMIsPipeline.wdl
+
+  - name: Testsnm3C
+    subclass: WDL
+    primaryDescriptorPath: /verification/test-wdls/Testsnm3C.wdl
+
+  - name: TestUltimaGenomicsJointGenotyping
+    subclass: WDL
+    primaryDescriptorPath: /verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl
+
+  - name: TestUltimaGenomicsWholeGenomeGermline
+    subclass: WDL
+    primaryDescriptorPath: /verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl
+
+  - name: TestUltimaGenomicsWholeGenomeCramOnly
+    subclass: WDL
+    primaryDescriptorPath: /verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl
+
+  - name: TestVariantCalling
+    subclass: WDL
+    primaryDescriptorPath: /verification/test-wdls/TestVariantCalling.wdl
+
+  - name: TestWholeGenomeGermlineSingleSample
+    subclass: WDL
+    primaryDescriptorPath: /verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl
+
+  - name: TestWholeGenomeReprocessing
+    subclass: WDL
+    primaryDescriptorPath: /verification/test-wdls/TestWholeGenomeReprocessing.wdl
+
   - name: VariantCalling
     subclass: WDL
     primaryDescriptorPath: /pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.wdl
 
   - name: SlideTags
     subclass: WDL
     primaryDescriptorPath: /beta-pipelines/skylab/slidetags/SlideTags.wdl
+
+  - name: TestATAC
+    subclass: WDL
+    primaryDescriptorPath: /verification/test-wdls/TestATAC.wdl

.github/workflows/test_atac.yml

@@ -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 }}

.github/workflows/test_cram_to_unmapped_bams.yml

@@ -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 }}

.github/workflows/test_exome_germline_single_sample.yml

@@ -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 }}