From 6e9963c17f5637c485de83a715853097ab914efd Mon Sep 17 00:00:00 2001 From: Jessica Way Date: Wed, 8 Jan 2025 09:51:54 -0700 Subject: [PATCH] Update output names for ReblockGVCF (#1443) * Update output names for ReblockGVCF --------- Co-authored-by: GitHub Action --- pipeline_versions.txt | 6 +++--- .../joint_genotyping/reblocking/ReblockGVCF.changelog.md | 5 +++++ .../germline/joint_genotyping/reblocking/ReblockGVCF.wdl | 6 +++--- .../ugwgs/UltimaGenomicsWholeGenomeGermline.changelog.md | 5 +++++ .../ugwgs/UltimaGenomicsWholeGenomeGermline.wdl | 6 +++--- .../BroadInternalUltimaGenomics.changelog.md | 5 +++++ .../UltimaGenomics/BroadInternalUltimaGenomics.wdl | 2 +- verification/test-wdls/TestReblockGVCF.wdl | 8 ++++---- 8 files changed, 29 insertions(+), 14 deletions(-) diff --git a/pipeline_versions.txt b/pipeline_versions.txt index 19b6185405..b24084e5fe 100644 --- a/pipeline_versions.txt +++ b/pipeline_versions.txt @@ -2,19 +2,19 @@ Pipeline Name Version Date of Last Commit CheckFingerprint 1.0.22 2024-10-28 RNAWithUMIsPipeline 1.0.18 2024-11-04 AnnotationFiltration 1.2.7 2024-11-04 -UltimaGenomicsWholeGenomeGermline 1.1.2 2024-11-04 +UltimaGenomicsWholeGenomeGermline 1.1.3 2024-12-05 WholeGenomeGermlineSingleSample 3.3.3 2024-11-04 ExomeGermlineSingleSample 3.2.3 2024-11-04 JointGenotypingByChromosomePartTwo 1.5.2 2024-11-04 JointGenotypingByChromosomePartOne 1.5.2 2024-11-04 -ReblockGVCF 2.3.2 2024-11-04 +ReblockGVCF 2.4.0 2024-12-05 JointGenotyping 1.7.2 2024-11-04 UltimaGenomicsJointGenotyping 1.2.2 2024-11-04 VariantCalling 2.2.4 2024-11-04 UltimaGenomicsWholeGenomeCramOnly 1.0.23 2024-11-04 GDCWholeGenomeSomaticSingleSample 1.3.4 2024-11-04 BroadInternalRNAWithUMIs 1.0.36 2024-11-04 -BroadInternalUltimaGenomics 1.1.2 2024-11-04 +BroadInternalUltimaGenomics 1.1.3 2024-12-05 BroadInternalArrays 1.1.14 2024-11-04 BroadInternalImputation 1.1.14 2024-11-04 Arrays 2.6.30 2024-11-04 diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.changelog.md b/pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.changelog.md index def54f5f09..545787cbbd 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.changelog.md +++ b/pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.changelog.md @@ -1,3 +1,8 @@ +# 2.4.0 +2024-12-05 (Date of Last Commit) + +* Updated output names for ReblockGVCF workflow from output_vcf and output_vcf_index to reblocked_gvcf and reblocked_gvcf_index respectively + # 2.3.2 2024-11-04 (Date of Last Commit) diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl b/pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl index 541c025e44..af577e894e 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl +++ b/pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl @@ -6,7 +6,7 @@ import "../../../../../../tasks/broad/Utilities.wdl" as utils workflow ReblockGVCF { - String pipeline_version = "2.3.2" + String pipeline_version = "2.4.0" input { @@ -70,8 +70,8 @@ workflow ReblockGVCF { } output { - File output_vcf = Reblock.output_vcf - File output_vcf_index = Reblock.output_vcf_index + File reblocked_gvcf = Reblock.output_vcf + File reblocked_gvcf_index = Reblock.output_vcf_index } meta { allowNestedInputs: true diff --git a/pipelines/broad/dna_seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.changelog.md b/pipelines/broad/dna_seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.changelog.md index 8e95e70d9e..07c3eab2ac 100644 --- a/pipelines/broad/dna_seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.changelog.md +++ b/pipelines/broad/dna_seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.changelog.md @@ -1,3 +1,8 @@ +# 1.1.3 +2024-12-05 (Date of Last Commit) + +* Updated the name of the output for ReblockGVCFs; this does not affect this pipeline + # 1.1.2 2024-11-04 (Date of Last Commit) diff --git a/pipelines/broad/dna_seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.wdl b/pipelines/broad/dna_seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.wdl index 48d0be5283..0e0a9e9bf3 100644 --- a/pipelines/broad/dna_seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.wdl +++ b/pipelines/broad/dna_seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.wdl @@ -50,7 +50,7 @@ workflow UltimaGenomicsWholeGenomeGermline { filtering_model_no_gt_name: "String describing the optional filtering model; default set to rf_model_ignore_gt_incl_hpol_runs" } - String pipeline_version = "1.1.2" + String pipeline_version = "1.1.3" References references = alignment_references.references @@ -202,8 +202,8 @@ workflow UltimaGenomicsWholeGenomeGermline { # Outputs that will be retained when execution is complete output { - File output_gvcf = ReblockGVCF.output_vcf - File output_gvcf_index = ReblockGVCF.output_vcf_index + File output_gvcf = ReblockGVCF.reblocked_gvcf + File output_gvcf_index = ReblockGVCF.reblocked_gvcf_index File output_vcf = ConvertGVCFtoVCF.output_vcf File output_vcf_index = ConvertGVCFtoVCF.output_vcf_index diff --git a/pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.changelog.md b/pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.changelog.md index 1375589cbd..fa1e432b84 100644 --- a/pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.changelog.md +++ b/pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.changelog.md @@ -1,3 +1,8 @@ +# 1.1.3 +2024-12-05 (Date of Last Commit) + +* Updated the name of the output for ReblockGVCFs; this does not affect this pipeline + # 1.1.2 2024-11-04 (Date of Last Commit) diff --git a/pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl b/pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl index 7c8ea24a44..6b5bdcfe7c 100644 --- a/pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl +++ b/pipelines/broad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl @@ -6,7 +6,7 @@ import "../../../../../../../pipelines/broad/qc/CheckFingerprint.wdl" as FP workflow BroadInternalUltimaGenomics { - String pipeline_version = "1.1.2" + String pipeline_version = "1.1.3" input { diff --git a/verification/test-wdls/TestReblockGVCF.wdl b/verification/test-wdls/TestReblockGVCF.wdl index 01607636c7..e35ccad0af 100644 --- a/verification/test-wdls/TestReblockGVCF.wdl +++ b/verification/test-wdls/TestReblockGVCF.wdl @@ -54,8 +54,8 @@ workflow TestReblockGVCF { # Collect all of the pipeline outputs into single Array[String] Array[String] pipeline_outputs = flatten([ [ # File outputs - ReblockGVCF.output_vcf_index, - ReblockGVCF.output_vcf, + ReblockGVCF.reblocked_gvcf_index, + ReblockGVCF.reblocked_gvcf, ], ]) @@ -86,13 +86,13 @@ workflow TestReblockGVCF { if (!update_truth){ call Utilities.GetValidationInputs as GetGvcf { input: - input_file = ReblockGVCF.output_vcf, + input_file = ReblockGVCF.reblocked_gvcf, results_path = results_path, truth_path = truth_path } call Utilities.GetValidationInputs as GetGvcfIndex { input: - input_file = ReblockGVCF.output_vcf_index, + input_file = ReblockGVCF.reblocked_gvcf_index, results_path = results_path, truth_path = truth_path }