From 759a3cb6bfa6dc14c6bf4936c33d8d636b21a42c Mon Sep 17 00:00:00 2001 From: npetrill Date: Thu, 20 Feb 2025 15:16:59 -0500 Subject: [PATCH] adding commenting to dependencies block --- .github/workflows/test_atac.yml | 6 ++++++ .github/workflows/test_cram_to_unmapped_bams.yml | 8 +++++++- .../workflows/test_exome_germline_single_sample.yml | 6 ++++++ .github/workflows/test_exome_reprocessing.yml | 6 ++++++ .github/workflows/test_illumina_genotyping_array.yml | 6 ++++++ .github/workflows/test_imputation.yml | 6 ++++++ .github/workflows/test_joint_genotyping.yml | 6 ++++++ .github/workflows/test_multiome.yml | 8 +++++++- .../test_multisamplesmartseq2singlenucleus.yml | 3 ++- .github/workflows/test_optimus.yml | 6 ++++++ .github/workflows/test_pairedtag.yml | 6 ++++++ .github/workflows/test_reblockGVCF.yml | 6 ++++++ .github/workflows/test_rna_with_umis.yml | 6 ++++++ .github/workflows/test_slideseq.yml | 6 ++++++ .github/workflows/test_snm3c.yml | 3 ++- .../test_ultima_genomics_joint_genotyping.yml | 6 ++++++ .../test_ultima_genomics_whole_genome_cram_only.yml | 7 ++++++- .../test_ultima_genomics_whole_genome_germline.yml | 7 ++++++- .github/workflows/test_variant_calling.yml | 10 ++++++++-- .../test_whole_genome_germline_single_sample.yml | 8 +++++++- .github/workflows/test_whole_genome_reprocessing.yml | 8 +++++++- 21 files changed, 124 insertions(+), 10 deletions(-) diff --git a/.github/workflows/test_atac.yml b/.github/workflows/test_atac.yml index af43f7878c..1962068303 100644 --- 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 index b4fb1672a7..952ac0aa5f 100644 --- 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 index f1f3dd861e..c5f9763f59 100644 --- 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 index c778512915..a5e3976eb5 100644 --- 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 index 6b503f5bc9..2250b2e281 100644 --- 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 index f24fb81673..629cd00f9f 100644 --- 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 index 3392272403..f2122fed0e 100644 --- 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 index 48501ee5ce..831aabf270 100644 --- 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 index 503e0ddd76..d420e6575f 100644 --- 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 index 62b55d630d..ae2418705c 100644 --- 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 index abab8767b0..37f53630e7 100644 --- 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 index 6ed282af0a..92be99d298 100644 --- 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 index 9bc62c99fa..82debfaa18 100644 --- 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 index c64a8cc385..ee66e000ea 100644 --- a/.github/workflows/test_slideseq.yml +++ b/.github/workflows/test_slideseq.yml @@ -9,7 +9,9 @@ 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' @@ -17,12 +19,16 @@ on: - '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 index 4f21a84888..f22a88ae00 100644 --- 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 index 4a37ddb3b0..d37674c7fd 100644 --- a/.github/workflows/test_ultima_genomics_joint_genotyping.yml +++ b/.github/workflows/test_ultima_genomics_joint_genotyping.yml @@ -9,11 +9,15 @@ 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' @@ -21,8 +25,10 @@ on: - '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 diff --git a/.github/workflows/test_ultima_genomics_whole_genome_cram_only.yml b/.github/workflows/test_ultima_genomics_whole_genome_cram_only.yml index 8e7644e013..25439c9a99 100644 --- a/.github/workflows/test_ultima_genomics_whole_genome_cram_only.yml +++ b/.github/workflows/test_ultima_genomics_whole_genome_cram_only.yml @@ -9,8 +9,9 @@ on: # SET PIPELINE SPECIFIC PATHS HERE # #################################### paths: + # anything in the pipelines folder - 'pipelines/broad/dna_seq/somatic/single_sample/ugwgs/**' - - 'pipelines/broad/dna_seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.wdl' + # tasks from the pipeline WDL and their dependencies - 'tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl' - 'tasks/broad/GermlineVariantDiscovery.wdl' - 'structs/dna_seq/DNASeqStructs.wdl' @@ -21,15 +22,19 @@ on: - 'tasks/broad/InternalTasks.wdl' - 'tasks/broad/UltimaGenomicsWholeGenomeGermlineAlignmentMarkDuplicates.wdl' - 'pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl' + # verification WDL and its dependencies - 'verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl' - 'verification/VerifyMetrics.wdl' - 'verification/VerifyTasks.wdl' - 'verification/VerifyNA12878.wdl' + # test WDL and its dependencies - 'verification/test-wdls/TestUltimaGenomicsWholeGenomeCramOnly.wdl' - 'tasks/broad/Utilities.wdl' - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl' + # this file, the subworkflow file, and the firecloud_api script - '.github/workflows/test_ultima_genomics_whole_genome_cram_only.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_whole_genome_germline.yml b/.github/workflows/test_ultima_genomics_whole_genome_germline.yml index 8da601d360..2f7acc0193 100644 --- a/.github/workflows/test_ultima_genomics_whole_genome_germline.yml +++ b/.github/workflows/test_ultima_genomics_whole_genome_germline.yml @@ -9,8 +9,9 @@ on: # SET PIPELINE SPECIFIC PATHS HERE # #################################### paths: + # anything in the pipelines folder - 'pipelines/broad/dna_seq/germline/single_sample/ugwgs/**' - - 'pipelines/broad/dna_seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.wdl' + # tasks from the pipeline WDL and their dependencies - 'tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl' - 'tasks/broad/GermlineVariantDiscovery.wdl' - 'structs/dna_seq/DNASeqStructs.wdl' @@ -21,15 +22,19 @@ on: - 'tasks/broad/InternalTasks.wdl' - 'tasks/broad/UltimaGenomicsWholeGenomeGermlineAlignmentMarkDuplicates.wdl' - 'pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl' + # verification WDL and its dependencies - 'verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl' - 'verification/VerifyMetrics.wdl' - 'verification/VerifyTasks.wdl' - 'verification/VerifyNA12878.wdl' + # test WDL and its dependencies - 'verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl' - 'tasks/broad/Utilities.wdl' - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl' + # this file, the subworkflow file, and the firecloud_api script - '.github/workflows/test_ultima_genomics_whole_genome_germline.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_variant_calling.yml b/.github/workflows/test_variant_calling.yml index 99abaaa64b..2f5f41cd92 100644 --- a/.github/workflows/test_variant_calling.yml +++ b/.github/workflows/test_variant_calling.yml @@ -9,18 +9,24 @@ on: # SET PIPELINE SPECIFIC PATHS HERE # #################################### paths: + # anything in the pipelines folder - 'pipelines/broad/dna_seq/germline/variant_calling/**' + # tasks from the pipeline WDL and their dependencies - 'tasks/broad/GermlineVariantDiscovery.wdl' - 'tasks/broad/Qc.wdl' - 'tasks/broad/Utilities.wdl' - 'tasks/broad/BamProcessing.wdl' - 'tasks/broad/DragenTasks.wdl' - - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl' - - 'verification/test-wdls/TestVariantCalling.wdl' + # verification WDL and its dependencies - 'verification/VerifyGvcf.wdl' - 'verification/VerifyTasks.wdl' + # test WDL and its dependencies + - 'verification/test-wdls/TestVariantCalling.wdl' + - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl' + # this file, the subworkflow file, and the firecloud_api script - '.github/workflows/test_variant_calling.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_whole_genome_germline_single_sample.yml b/.github/workflows/test_whole_genome_germline_single_sample.yml index 9752d70bef..c79c30de75 100644 --- a/.github/workflows/test_whole_genome_germline_single_sample.yml +++ b/.github/workflows/test_whole_genome_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/wgs/**' + # tasks from the pipeline WDL and their dependencies - 'structs/dna_seq/DNASeqStructs.wdl' - 'tasks/broad/Alignment.wdl' - 'tasks/broad/DragmapAlignment.wdl' @@ -22,13 +24,17 @@ on: - 'pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.wdl' - 'tasks/broad/GermlineVariantDiscovery.wdl' - 'tasks/broad/DragenTasks.wdl' - - 'verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl' + # verification WDL and its dependencies - 'verification/VerifyGermlineSingleSample.wdl' - 'verification/VerifyMetrics.wdl' - 'verification/VerifyTasks.wdl' + # test WDL and its dependencies + - 'verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl' - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl' + # this file, the subworkflow file, and the firecloud_api script - '.github/workflows/test_whole_genome_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_whole_genome_reprocessing.yml b/.github/workflows/test_whole_genome_reprocessing.yml index ed6494df77..0abff328cc 100644 --- a/.github/workflows/test_whole_genome_reprocessing.yml +++ b/.github/workflows/test_whole_genome_reprocessing.yml @@ -9,8 +9,10 @@ on: # SET PIPELINE SPECIFIC PATHS HERE # #################################### paths: + # anything in the pipelines folder - 'pipelines/broad/reprocessing/wgs/**' - 'pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl' + # tasks from the pipeline WDL and their dependencies - 'structs/dna_seq/DNASeqStructs.wdl' - 'tasks/broad/Alignment.wdl' - 'tasks/broad/DragmapAlignment.wdl' @@ -24,14 +26,18 @@ on: - 'pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl' - 'tasks/broad/GermlineVariantDiscovery.wdl' - 'tasks/broad/DragenTasks.wdl' + # verification WDL and its dependencies - 'verification/VerifyExomeReprocessing.wdl' - - 'verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl' - 'verification/VerifyGermlineSingleSample.wdl' - 'verification/VerifyMetrics.wdl' - 'verification/VerifyTasks.wdl' + # test WDL and its dependencies + - 'verification/test-wdls/TestWholeGenomeGermlineSingleSample.wdl' - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl' + # this file, the subworkflow file, and the firecloud_api script - '.github/workflows/test_whole_genome_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