Merge remote-tracking branch 'origin/np_address_github_terra_delay_1'…

… into np_address_github_terra_delay_1
broadinstitute · Feb 21, 2025 · 6dae8b5 · 6dae8b5
2 parents 4bbb312 + 0d8d721
commit 6dae8b5
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Showing 25 changed files with 133 additions and 36 deletions.
diff --git a/.github/workflows/test_atac.yml b/.github/workflows/test_atac.yml
@@ -9,17 +9,23 @@ on:
     # 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

diff --git a/.github/workflows/test_cram_to_unmapped_bams.yml b/.github/workflows/test_cram_to_unmapped_bams.yml
@@ -9,13 +9,19 @@ on:
     # 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/Utilities.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

diff --git a/.github/workflows/test_exome_germline_single_sample.yml b/.github/workflows/test_exome_germline_single_sample.yml
@@ -9,7 +9,9 @@ on:
     # 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'
@@ -22,13 +24,17 @@ on:
       - '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

diff --git a/.github/workflows/test_exome_reprocessing.yml b/.github/workflows/test_exome_reprocessing.yml
@@ -9,9 +9,11 @@ on:
     # SET PIPELINE SPECIFIC PATHS HERE #
     ####################################
     paths:
+      # anything in the pipelines folder
      - 'pipelines/broad/reprocessing/exome/**'
      - 'pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl'
      - 'pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl'
+      # tasks from the pipeline WDL and their dependencies
      - 'tasks/broad/UnmappedBamToAlignedBam.wdl'
      - 'tasks/broad/AggregatedBamQC.wdl'
      - 'tasks/broad/Qc.wdl'
@@ -24,14 +26,18 @@ on:
      - 'tasks/broad/DragenTasks.wdl'
      - 'tasks/broad/Qc.wdl'
      - 'tasks/broad/Utilities.wdl'
+      # verification WDL and its dependencies
      - 'verification/VerifyExomeReprocessing.wdl'
      - 'verification/VerifyGermlineSingleSample.wdl'
+      # test WDL and its dependencies
      - 'verification/test-wdls/TestCramToUnmappedBams.wdl'
      - 'verification/VerifyMetrics.wdl'
      - 'verification/VerifyTasks.wdl'
      - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl'
+      # this file, the subworkflow file, and the firecloud_api script
      - '.github/workflows/test_exome_reprocessing.yml'
      - '.github/workflows/warp_test_workflow.yml'
+     - 'scripts/firecloud_api/firecloud_api.py'
 
 
   # Allows you to run this workflow manually from the Actions tab

diff --git a/.github/workflows/test_illumina_genotyping_array.yml b/.github/workflows/test_illumina_genotyping_array.yml
@@ -9,15 +9,21 @@ on:
     # SET PIPELINE SPECIFIC PATHS HERE #
     ####################################
     paths:
+      # anything in the pipelines folder
       - 'pipelines/broad/genotyping/illumina/**'
+      # tasks from the pipeline WDL and their dependencies
       - 'tasks/broad/IlluminaGenotypingArrayTasks.wdl'
       - 'tasks/broad/Qc.wdl'
+      # verification WDL and its dependencies
       - 'verification/VerifyIlluminaGenotypingArray.wdl'
+      # test WDL and its dependencies
       - 'verification/test-wdls/TestIlluminaGenotypingArray.wdl'
       - 'tasks/broad/Utilities.wdl'
       - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl'
+      # this file, the subworkflow file, and the firecloud_api script
       - '.github/workflows/test_illumina_genotyping_array.yml'
       - '.github/workflows/warp_test_workflow.yml'
+      - 'scripts/firecloud_api/firecloud_api.py'
 
 
   # Allows you to run this workflow manually from the Actions tab

diff --git a/.github/workflows/test_imputation.yml b/.github/workflows/test_imputation.yml
@@ -9,15 +9,21 @@ on:
     # SET PIPELINE SPECIFIC PATHS HERE #
     ####################################
     paths:
+      # anything in the pipelines folder
       - 'pipelines/broad/arrays/imputation/**'
       - 'structs/imputation/ImputationStructs.wdl'
+      # tasks from the pipeline WDL and their dependencies
       - 'tasks/broad/ImputationTasks.wdl'
+      # verification WDL and its dependencies
       - 'verification/VerifyImputation.wdl'
+      # test WDL and its dependencies
       - 'verification/test-wdls/TestImputation.wdl'
       - 'tasks/broad/Utilities.wdl'
       - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl'
+      # this file, the subworkflow file, and the firecloud_api script
       - '.github/workflows/test_imputation.yml'
       - '.github/workflows/warp_test_workflow.yml'
+      - 'scripts/firecloud_api/firecloud_api.py'
 
 
   # Allows you to run this workflow manually from the Actions tab

diff --git a/.github/workflows/test_joint_genotyping.yml b/.github/workflows/test_joint_genotyping.yml
@@ -9,18 +9,24 @@ on:
     # SET PIPELINE SPECIFIC PATHS HERE #
     ####################################
     paths:
+      # anything in the pipelines folder
       - 'pipelines/broad/dna_seq/germline/joint_genotyping/**'
+      # tasks from the pipeline WDL and their dependencies
       - 'tasks/broad/JointGenotypingTasks.wdl'
+      # verification WDL and its dependencies
       - 'verification/VerifyJointGenotyping.wdl'
       - 'verification/VerifyTasks.wdl'
       - 'verification/VerifyMetrics.wdl'
       - 'verification/VerifyGermlineSingleSample.wdl'
       - 'verification/VerifyNA12878.wdl'
+      # test WDL and its dependencies
       - 'verification/test-wdls/TestJointGenotyping.wdl'
       - 'tasks/broad/Utilities.wdl'
       - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl'
+      # this file, the subworkflow file, and the firecloud_api script
       - '.github/workflows/test_joint_genotyping.yml'
       - '.github/workflows/warp_test_workflow.yml'
+      - 'scripts/firecloud_api/firecloud_api.py'
 
 
   # Allows you to run this workflow manually from the Actions tab

diff --git a/.github/workflows/test_multiome.yml b/.github/workflows/test_multiome.yml
@@ -9,7 +9,9 @@ on:
     # SET PIPELINE SPECIFIC PATHS HERE #
     ####################################
     paths:
+      # anything in the pipelines folder
       - 'pipelines/skylab/multiome/**'
+      # tasks from the pipeline WDL and their dependencies
       - 'tasks/skylab/MergeSortBam.wdl'
       - 'tasks/skylab/FastqProcessing.wdl'
       - 'tasks/skylab/PairedTagUtils.wdl'
@@ -23,11 +25,15 @@ on:
       - 'tasks/skylab/H5adUtils.wdl'
       - 'tasks/broad/Utilities.wdl'
       - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl'
-      - '.github/workflows/test_multiome.yml'
+      # verification WDL and its dependencies
       - 'verification/VerifyMultiome.wdl'
       - 'verification/VerifyTasks.wdl'
+      # test WDL and its dependencies
       - 'verification/test-wdls/TestMultiome.wdl'
+      # this file, the subworkflow file, and the firecloud_api script
+      - '.github/workflows/test_multiome.yml'
       - '.github/workflows/warp_test_workflow.yml'
+      - 'scripts/firecloud_api/firecloud_api.py'
 
 
   # Allows you to run this workflow manually from the Actions tab

diff --git a/.github/workflows/test_multisamplesmartseq2singlenucleus.yml b/.github/workflows/test_multisamplesmartseq2singlenucleus.yml
@@ -24,9 +24,10 @@ on:
       # test WDL and its dependencies
       - 'verification/test-wdls/TestMultiSampleSmartSeq2SingleNucleus.wdl'
       - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl'
-      # this file and the subworkflow file
+      # this file, the subworkflow file, and the firecloud_api script
       - '.github/workflows/test_multisamplesmartseq2singlenucleus.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:

diff --git a/.github/workflows/test_optimus.yml b/.github/workflows/test_optimus.yml
@@ -9,7 +9,9 @@ on:
     # SET PIPELINE SPECIFIC PATHS HERE #
     ####################################
     paths:
+      # anything in the pipelines folder
       - 'pipelines/skylab/optimus/**'
+      # tasks from the pipeline WDL and their dependencies
       - 'tasks/skylab/FastqProcessing.wdl'
       - 'tasks/skylab/StarAlign.wdl'
       - 'tasks/skylab/Metrics.wdl'
@@ -18,13 +20,17 @@ on:
       - 'tasks/skylab/MergeSortBam.wdl'
       - 'tasks/skylab/H5adUtils.wdl'
       - 'tasks/broad/Utilities.wdl'
+      # verification WDL and its dependencies
       - 'verification/VerifyOptimus.wdl'
       - 'verification/VerifyTasks.wdl'
+      # test WDL and its dependencies
       - 'verification/test-wdls/TestOptimus.wdl'
       - 'tasks/broad/Utilities.wdl'
       - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl'
+      # this file, the subworkflow file, and the firecloud_api script
       - '.github/workflows/test_optimus.yml'
       - '.github/workflows/warp_test_workflow.yml'
+      - 'scripts/firecloud_api/firecloud_api.py'
 
 
   # Allows you to run this workflow manually from the Actions tab

diff --git a/.github/workflows/test_pairedtag.yml b/.github/workflows/test_pairedtag.yml
@@ -9,8 +9,10 @@ on:
     # SET PIPELINE SPECIFIC PATHS HERE #
     ####################################
     paths:
+      # anything in the pipelines folder
       - 'pipelines/skylab/paired_tag/**'
       - 'pipelines/skylab/optimus/Optimus.wdl'
+      # tasks from the pipeline WDL and their dependencies
       - 'tasks/skylab/H5adUtils.wdl'
       - 'tasks/skylab/PairedTagUtils.wdl'
       - 'tasks/broad/Utilities.wdl'
@@ -20,13 +22,17 @@ on:
       - 'tasks/skylab/RunEmptyDrops.wdl'
       - 'tasks/skylab/CheckInputs.wdl'
       - 'tasks/skylab/MergeSortBam.wdl'
+      # verification WDL and its dependencies
       - 'verification/VerifyPairedTag.wdl'
       - 'verification/VerifyTasks.wdl'
+      # test WDL and its dependencies
       - 'verification/test-wdls/TestPairedTag.wdl'
       - 'tasks/broad/Utilities.wdl'
       - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl'
+      # this file, the subworkflow file, and the firecloud_api script
       - '.github/workflows/test_pairedtag.yml'
       - '.github/workflows/warp_test_workflow.yml'
+      - 'scripts/firecloud_api/firecloud_api.py'
 
 
   # Allows you to run this workflow manually from the Actions tab

diff --git a/.github/workflows/test_reblockGVCF.yml b/.github/workflows/test_reblockGVCF.yml
@@ -9,16 +9,22 @@ on:
     # SET PIPELINE SPECIFIC PATHS HERE #
     ####################################
     paths:
+      # anything in the pipelines folder
       - 'pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/**'
+      # tasks from the pipeline WDL and their dependencies
       - 'tasks/broad/GermlineVariantDiscovery.wdl'
       - 'tasks/broad/Qc.wdl'
       - 'tasks/broad/Utilities.wdl'
+      # verification WDL and its dependencies
       - 'verification/VerifyGvcf.wdl'
       - 'verification/VerifyTasks.wdl'
+      # test WDL and its dependencies
       - 'verification/test-wdls/TestReblockGVCF.wdl'
       - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl'
+      # this file, the subworkflow file, and the firecloud_api script
       - '.github/workflows/test_reblockGVCF.yml'
       - '.github/workflows/warp_test_workflow.yml'
+      - 'scripts/firecloud_api/firecloud_api.py'
 
 
   # Allows you to run this workflow manually from the Actions tab

diff --git a/.github/workflows/test_rna_with_umis.yml b/.github/workflows/test_rna_with_umis.yml
@@ -9,17 +9,23 @@ on:
     # SET PIPELINE SPECIFIC PATHS HERE #
     ####################################
     paths:
+      # anything in the pipelines folder
       - 'pipelines/broad/rna_seq/**'
+      # tasks from the pipeline WDL and their dependencies
       - 'tasks/broad/UMIAwareDuplicateMarking.wdl'
       - 'tasks/broad/RNAWithUMIsTasks.wdl'
       - 'tasks/broad/Utilities.wdl'
+      # verification WDL and its dependencies
       - 'verification/VerifyRNAWithUMIs.wdl'
       - 'verification/VerifyMetrics.wdl'
       - 'verification/VerifyTasks.wdl'
+      # test WDL and its dependencies
       - 'verification/test-wdls/TestRNAWithUMIsPipeline.wdl'
       - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl'
+      # this file, the subworkflow file, and the firecloud_api script
       - '.github/workflows/test_rna_with_umis.yml'
       - '.github/workflows/warp_test_workflow.yml'
+      - 'scripts/firecloud_api/firecloud_api.py'
 
 
   # Allows you to run this workflow manually from the Actions tab

diff --git a/.github/workflows/test_slideseq.yml b/.github/workflows/test_slideseq.yml
@@ -9,20 +9,26 @@ on:
     # 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

diff --git a/.github/workflows/test_snm3c.yml b/.github/workflows/test_snm3c.yml
@@ -18,9 +18,10 @@ on:
       # test WDL and its dependencies
       - 'verification/test-wdls/Testsnm3C.wdl'
       - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl'
-      # this file and the subworkflow file
+      # this file, the subworkflow file, and the firecloud_api script
       - '.github/workflows/test_snm3c.yml'
       - '.github/workflows/warp_test_workflow.yml'
+      - 'scripts/firecloud_api/firecloud_api.py'
 
 
   # Allows you to run this workflow manually from the Actions tab

diff --git a/.github/workflows/test_ultima_genomics_joint_genotyping.yml b/.github/workflows/test_ultima_genomics_joint_genotyping.yml
@@ -9,20 +9,26 @@ on:
     # SET PIPELINE SPECIFIC PATHS HERE #
     ####################################
     paths:
+      # anything in the pipelines folder
       - 'pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/**'
+      # tasks from the pipeline WDL and their dependencies
       - 'tasks/broad/JointGenotypingTasks.wdl'
       - 'tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl'
       - 'tasks/broad/JointGenotypingTasks.wdl'
+      # verification WDL and its dependencies
       - 'verification/VerifyUltimaGenomicsJointGenotyping.wdl'
+      # test WDL and its dependencies
       - 'verification/test-wdls/TestUltimaGenomicsJointGenotyping.wdl'
       - 'verification/VerifyTasks.wdl'
       - 'verification/VerifyMetrics.wdl'
       - 'verification/VerifyGermlineSingleSample.wdl'
       - 'verification/VerifyNA12878.wdl'
       - 'tasks/broad/Utilities.wdl'
       - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl'
+      # this file, the subworkflow file, and the firecloud_api script
       - '.github/workflows/test_ultima_genomics_joint_genotyping.yml'
       - '.github/workflows/warp_test_workflow.yml'
+      - 'scripts/firecloud_api/firecloud_api.py'
 
 
   # Allows you to run this workflow manually from the Actions tab