From d7c2443b622601ed79ff67381aed69a55abb439c Mon Sep 17 00:00:00 2001 From: Nikelle Petrillo <38223776+nikellepetrillo@users.noreply.github.com> Date: Tue, 5 Nov 2024 17:13:31 -0500 Subject: [PATCH] Np update gatk 4.6.1.0 revert bqsr and validate chip (#1405) * gatk docker update * gatk docker update * revert bqsr to gstk 4.3 * revert genotypeconcordance to gstk 4.3 * revert genotypeconcordance to gstk 4.3 * add megans commit * add megans commit * fix names of inputs for CompareVCFsVerbosely * fix names of inputs for CompareVCFsVerbosely * hook up index files * missed some test inputs * changelogs and versions * Updated pipeline_versions.txt with all pipeline version information * changelogs * Updated pipeline_versions.txt with all pipeline version information * changelogs * Updated pipeline_versions.txt with all pipeline version information --------- Co-authored-by: GitHub Action --- pipeline_versions.txt | 50 +++++++++---------- .../AnnotationFiltration.changelog.md | 5 ++ .../AnnotationFiltration.wdl | 4 +- .../test_inputs/Plumbing/hg38.json | 2 +- .../test_inputs/Scientific/hg38.json | 2 +- .../arrays/imputation/Imputation.changelog.md | 5 ++ .../broad/arrays/imputation/Imputation.wdl | 2 +- .../arrays/single_sample/Arrays.changelog.md | 5 ++ .../broad/arrays/single_sample/Arrays.wdl | 2 +- .../validate_chip/ValidateChip.changelog.md | 5 ++ .../arrays/validate_chip/ValidateChip.wdl | 2 +- .../JointGenotyping.changelog.md | 5 ++ .../joint_genotyping/JointGenotyping.wdl | 4 +- ...UltimaGenomicsJointGenotyping.changelog.md | 5 ++ .../UltimaGenomicsJointGenotyping.wdl | 6 +-- ...GenotypingByChromosomePartOne.changelog.md | 5 ++ .../JointGenotypingByChromosomePartOne.wdl | 2 +- ...GenotypingByChromosomePartTwo.changelog.md | 5 ++ .../JointGenotypingByChromosomePartTwo.wdl | 2 +- .../reblocking/ReblockGVCF.changelog.md | 5 ++ .../reblocking/ReblockGVCF.wdl | 6 +-- .../ExomeGermlineSingleSample.changelog.md | 5 ++ .../exome/ExomeGermlineSingleSample.wdl | 6 +-- ...maGenomicsWholeGenomeGermline.changelog.md | 5 ++ .../UltimaGenomicsWholeGenomeGermline.wdl | 2 +- ...oleGenomeGermlineSingleSample.changelog.md | 5 ++ .../wgs/WholeGenomeGermlineSingleSample.wdl | 2 +- .../VariantCalling.changelog.md | 5 ++ .../variant_calling/VariantCalling.wdl | 6 +-- ...maGenomicsWholeGenomeCramOnly.changelog.md | 5 ++ .../UltimaGenomicsWholeGenomeCramOnly.wdl | 2 +- ...holeGenomeSomaticSingleSample.changelog.md | 5 ++ .../GDCWholeGenomeSomaticSingleSample.wdl | 6 +-- .../IlluminaGenotypingArray.changelog.md | 5 ++ .../illumina/IlluminaGenotypingArray.wdl | 2 +- .../BroadInternalImputation.changelog.md | 5 ++ .../imputation/BroadInternalImputation.wdl | 2 +- .../BroadInternalArrays.changelog.md | 5 ++ .../single_sample/BroadInternalArrays.wdl | 2 +- .../BroadInternalUltimaGenomics.changelog.md | 5 ++ .../BroadInternalUltimaGenomics.wdl | 2 +- .../BroadInternalRNAWithUMIs.changelog.md | 5 ++ .../rna_seq/BroadInternalRNAWithUMIs.wdl | 2 +- .../exome/ExomeReprocessing.changelog.md | 5 ++ .../reprocessing/exome/ExomeReprocessing.wdl | 2 +- .../ExternalExomeReprocessing.changelog.md | 5 ++ .../exome/ExternalExomeReprocessing.wdl | 2 +- ...ternalWholeGenomeReprocessing.changelog.md | 5 ++ .../wgs/ExternalWholeGenomeReprocessing.wdl | 2 +- .../wgs/WholeGenomeReprocessing.changelog.md | 5 ++ .../wgs/WholeGenomeReprocessing.wdl | 2 +- .../rna_seq/RNAWithUMIsPipeline.changelog.md | 5 ++ .../broad/rna_seq/RNAWithUMIsPipeline.wdl | 2 +- scripts/BuildAFComparisonTable.wdl | 10 ++-- scripts/RemoveBadSitesByID.wdl | 4 +- tasks/broad/CheckContaminationSomatic.wdl | 2 +- tasks/broad/DragenTasks.wdl | 2 +- tasks/broad/GermlineVariantDiscovery.wdl | 8 +-- tasks/broad/IlluminaGenotypingArrayTasks.wdl | 8 +-- tasks/broad/ImputationTasks.wdl | 16 +++--- tasks/broad/JointGenotypingTasks.wdl | 34 ++++++------- tasks/broad/RNAWithUMIsTasks.wdl | 10 ++-- ...timaGenomicsGermlineFilteringThreshold.wdl | 4 +- ...UltimaGenomicsWholeGenomeGermlineTasks.wdl | 12 ++--- verification/VerifyNA12878.wdl | 2 +- .../VerifyUltimaGenomicsJointGenotyping.wdl | 11 ++++ ...erifyUltimaGenomicsWholeGenomeGermline.wdl | 13 +++++ .../TestBroadInternalUltimaGenomics.wdl | 8 +++ .../TestUltimaGenomicsWholeGenomeGermline.wdl | 9 ++++ 69 files changed, 286 insertions(+), 120 deletions(-) diff --git a/pipeline_versions.txt b/pipeline_versions.txt index 523a909195..d3653a5a97 100644 --- a/pipeline_versions.txt +++ b/pipeline_versions.txt @@ -1,32 +1,32 @@ Pipeline Name Version Date of Last Commit CheckFingerprint 1.0.22 2024-10-28 -RNAWithUMIsPipeline 1.0.17 2024-09-06 -AnnotationFiltration 1.2.6 2024-09-06 -UltimaGenomicsWholeGenomeGermline 1.1.1 2024-10-28 -WholeGenomeGermlineSingleSample 3.3.2 2024-10-28 -ExomeGermlineSingleSample 3.2.2 2024-10-28 -JointGenotypingByChromosomePartTwo 1.5.1 2024-09-10 -JointGenotypingByChromosomePartOne 1.5.1 2024-09-10 -ReblockGVCF 2.3.1 2024-10-28 -JointGenotyping 1.7.1 2024-09-10 -UltimaGenomicsJointGenotyping 1.2.1 2024-09-10 -VariantCalling 2.2.3 2024-10-28 -UltimaGenomicsWholeGenomeCramOnly 1.0.22 2024-10-28 -GDCWholeGenomeSomaticSingleSample 1.3.3 2024-09-06 -BroadInternalRNAWithUMIs 1.0.35 2024-09-06 -BroadInternalUltimaGenomics 1.1.1 2024-10-28 -BroadInternalArrays 1.1.13 2024-10-28 -BroadInternalImputation 1.1.13 2024-09-06 -Arrays 2.6.29 2024-10-28 -ValidateChip 1.16.6 2024-09-06 +RNAWithUMIsPipeline 1.0.18 2024-11-04 +AnnotationFiltration 1.2.7 2024-11-04 +UltimaGenomicsWholeGenomeGermline 1.1.2 2024-11-04 +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 +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 +BroadInternalArrays 1.1.14 2024-11-04 +BroadInternalImputation 1.1.14 2024-11-04 +Arrays 2.6.30 2024-11-04 +ValidateChip 1.16.7 2024-11-04 MultiSampleArrays 1.6.2 2024-08-02 -Imputation 1.1.14 2024-09-06 -IlluminaGenotypingArray 1.12.23 2024-10-28 -ExternalWholeGenomeReprocessing 2.3.2 2024-10-28 -ExternalExomeReprocessing 3.3.2 2024-10-28 +Imputation 1.1.15 2024-11-04 +IlluminaGenotypingArray 1.12.24 2024-11-04 +ExternalWholeGenomeReprocessing 2.3.3 2024-11-04 +ExternalExomeReprocessing 3.3.3 2024-11-04 CramToUnmappedBams 1.1.3 2024-08-02 -WholeGenomeReprocessing 3.3.2 2024-10-28 -ExomeReprocessing 3.3.2 2024-10-28 +WholeGenomeReprocessing 3.3.3 2024-11-04 +ExomeReprocessing 3.3.3 2024-11-04 BuildIndices 3.0.0 2023-12-06 scATAC 1.3.2 2023-08-03 snm3C 4.0.4 2024-08-06 diff --git a/pipelines/broad/annotation_filtration/AnnotationFiltration.changelog.md b/pipelines/broad/annotation_filtration/AnnotationFiltration.changelog.md index a8cff3a2f4..4cdf13e71e 100644 --- a/pipelines/broad/annotation_filtration/AnnotationFiltration.changelog.md +++ b/pipelines/broad/annotation_filtration/AnnotationFiltration.changelog.md @@ -1,3 +1,8 @@ +# 1.2.7 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 1.2.6 2024-09-06 (Date of Last Commit) diff --git a/pipelines/broad/annotation_filtration/AnnotationFiltration.wdl b/pipelines/broad/annotation_filtration/AnnotationFiltration.wdl index 39bb552814..4e0280d93b 100644 --- a/pipelines/broad/annotation_filtration/AnnotationFiltration.wdl +++ b/pipelines/broad/annotation_filtration/AnnotationFiltration.wdl @@ -4,7 +4,7 @@ import "../../../tasks/broad/Funcotator.wdl" as Funcotator workflow AnnotationFiltration { - String pipeline_version = "1.2.6" + String pipeline_version = "1.2.7" input { Array[File] vcfs @@ -15,7 +15,7 @@ workflow AnnotationFiltration { File ref_dict File? funcotator_interval_list - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" File? custom_data_source_tar_gz } diff --git a/pipelines/broad/annotation_filtration/test_inputs/Plumbing/hg38.json b/pipelines/broad/annotation_filtration/test_inputs/Plumbing/hg38.json index d87a07c1ea..c8907ba8a2 100644 --- a/pipelines/broad/annotation_filtration/test_inputs/Plumbing/hg38.json +++ b/pipelines/broad/annotation_filtration/test_inputs/Plumbing/hg38.json @@ -10,6 +10,6 @@ "AnnotationFiltration.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai", "AnnotationFiltration.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict", - "AnnotationFiltration.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.5.0.0", + "AnnotationFiltration.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.6.1.0", "AnnotationFiltration.custom_data_source_tar_gz": "gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.6.20190124g.tar.gz" } diff --git a/pipelines/broad/annotation_filtration/test_inputs/Scientific/hg38.json b/pipelines/broad/annotation_filtration/test_inputs/Scientific/hg38.json index 6f36aeaafa..d4ab9d499b 100644 --- a/pipelines/broad/annotation_filtration/test_inputs/Scientific/hg38.json +++ b/pipelines/broad/annotation_filtration/test_inputs/Scientific/hg38.json @@ -8,6 +8,6 @@ "AnnotationFiltration.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai", "AnnotationFiltration.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict", - "AnnotationFiltration.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.5.0.0", + "AnnotationFiltration.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.6.1.0", "AnnotationFiltration.custom_data_source_tar_gz": "gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.6.20190124g.tar.gz" } diff --git a/pipelines/broad/arrays/imputation/Imputation.changelog.md b/pipelines/broad/arrays/imputation/Imputation.changelog.md index 5204fc480a..52765e4ec1 100644 --- a/pipelines/broad/arrays/imputation/Imputation.changelog.md +++ b/pipelines/broad/arrays/imputation/Imputation.changelog.md @@ -1,3 +1,8 @@ +# 1.1.15 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 1.1.14 2024-09-06 (Date of Last Commit) diff --git a/pipelines/broad/arrays/imputation/Imputation.wdl b/pipelines/broad/arrays/imputation/Imputation.wdl index cec0128b55..4a44ba4ac5 100644 --- a/pipelines/broad/arrays/imputation/Imputation.wdl +++ b/pipelines/broad/arrays/imputation/Imputation.wdl @@ -6,7 +6,7 @@ import "../../../../tasks/broad/Utilities.wdl" as utils workflow Imputation { - String pipeline_version = "1.1.14" + String pipeline_version = "1.1.15" input { Int chunkLength = 25000000 diff --git a/pipelines/broad/arrays/single_sample/Arrays.changelog.md b/pipelines/broad/arrays/single_sample/Arrays.changelog.md index 004aaace5a..653192dcba 100644 --- a/pipelines/broad/arrays/single_sample/Arrays.changelog.md +++ b/pipelines/broad/arrays/single_sample/Arrays.changelog.md @@ -1,3 +1,8 @@ +# 2.6.30 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 2.6.29 2024-10-28 (Date of Last Commit) diff --git a/pipelines/broad/arrays/single_sample/Arrays.wdl b/pipelines/broad/arrays/single_sample/Arrays.wdl index 72004afa3d..2313520358 100644 --- a/pipelines/broad/arrays/single_sample/Arrays.wdl +++ b/pipelines/broad/arrays/single_sample/Arrays.wdl @@ -23,7 +23,7 @@ import "../../../../tasks/broad/Utilities.wdl" as utils workflow Arrays { - String pipeline_version = "2.6.29" + String pipeline_version = "2.6.30" input { String chip_well_barcode diff --git a/pipelines/broad/arrays/validate_chip/ValidateChip.changelog.md b/pipelines/broad/arrays/validate_chip/ValidateChip.changelog.md index 04788bd150..f44c2c384d 100644 --- a/pipelines/broad/arrays/validate_chip/ValidateChip.changelog.md +++ b/pipelines/broad/arrays/validate_chip/ValidateChip.changelog.md @@ -1,3 +1,8 @@ +# 1.16.7 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 1.16.6 2024-09-06 (Date of Last Commit) diff --git a/pipelines/broad/arrays/validate_chip/ValidateChip.wdl b/pipelines/broad/arrays/validate_chip/ValidateChip.wdl index b6c03c19f0..111d8726a2 100644 --- a/pipelines/broad/arrays/validate_chip/ValidateChip.wdl +++ b/pipelines/broad/arrays/validate_chip/ValidateChip.wdl @@ -21,7 +21,7 @@ import "../../../../tasks/broad/InternalArraysTasks.wdl" as InternalTasks workflow ValidateChip { - String pipeline_version = "1.16.6" + String pipeline_version = "1.16.7" input { String sample_alias diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.changelog.md b/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.changelog.md index 590abe52ec..73e7ce98e8 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.changelog.md +++ b/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.changelog.md @@ -1,3 +1,8 @@ +# 1.7.2 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 1.7.1 2024-09-10 (Date of Last Commit) diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl b/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl index bf30156d98..48e5f5487d 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl +++ b/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl @@ -7,7 +7,7 @@ import "https://raw.githubusercontent.com/broadinstitute/gatk/4.5.0.0/scripts/vc # Joint Genotyping for hg38 Whole Genomes and Exomes (has not been tested on hg19) workflow JointGenotyping { - String pipeline_version = "1.7.1" + String pipeline_version = "1.7.2" input { File unpadded_intervals_file @@ -214,7 +214,7 @@ workflow JointGenotyping { extract_extra_args = extract_extra_args, resource_args = resource_args, output_prefix = callset_name, - gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" } } if (!run_vets) { diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.changelog.md b/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.changelog.md index 2b18b1a1c5..51889c45e8 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.changelog.md +++ b/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.changelog.md @@ -1,3 +1,8 @@ +# 1.2.2 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 1.2.1 2024-09-10 (Date of Last Commit) diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.wdl b/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.wdl index 06722fc971..9f998b220c 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.wdl +++ b/pipelines/broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.wdl @@ -11,7 +11,7 @@ import "../../../../../../tasks/broad/UltimaGenomicsGermlineFilteringThreshold.w # For choosing a filtering threshold (where on the ROC curve to filter) a sample with truth data is required. workflow UltimaGenomicsJointGenotyping { - String pipeline_version = "1.2.1" + String pipeline_version = "1.2.2" input { File unpadded_intervals_file @@ -168,7 +168,7 @@ workflow UltimaGenomicsJointGenotyping { extract_extra_args = "--mode SNP", train_extra_args = "--mode SNP", score_extra_args = "--mode SNP", - gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" } call Filtering.JointVcfFiltering as TrainAndApplyFilteringModelINDELs { @@ -184,7 +184,7 @@ workflow UltimaGenomicsJointGenotyping { extract_extra_args = "--mode INDEL", train_extra_args = "--mode INDEL", score_extra_args = "--mode INDEL", - gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" } call FilteringThreshold.ExtractOptimizeSingleSample as FindFilteringThresholdAndFilter { diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md index 162fcd033f..e6f6e0f5a6 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md +++ b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md @@ -1,3 +1,8 @@ +# 1.5.2 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 1.5.1 2024-09-10 (Date of Last Commit) diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl index cdcc1b49a5..6484c244cf 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl +++ b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl @@ -5,7 +5,7 @@ import "../../../../../../tasks/broad/JointGenotypingTasks.wdl" as Tasks # Joint Genotyping for hg38 Exomes and Whole Genomes (has not been tested on hg19) workflow JointGenotypingByChromosomePartOne { - String pipeline_version = "1.5.1" + String pipeline_version = "1.5.2" input { File unpadded_intervals_file diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.changelog.md b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.changelog.md index 1b4075e674..0d71cf5b40 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.changelog.md +++ b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.changelog.md @@ -1,3 +1,8 @@ +# 1.5.2 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 1.5.1 2024-09-10 (Date of Last Commit) diff --git a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl index 17d23047b0..23bd06cdea 100644 --- a/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl +++ b/pipelines/broad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl @@ -5,7 +5,7 @@ import "../../../../../../tasks/broad/JointGenotypingTasks.wdl" as Tasks # Joint Genotyping for hg38 Exomes and Whole Genomes (has not been tested on hg19) workflow JointGenotypingByChromosomePartTwo { - String pipeline_version = "1.5.1" + String pipeline_version = "1.5.2" input { String callset_name 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 27f3b07cfb..def54f5f09 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 @@ +# 2.3.2 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 2.3.1 2024-10-28 (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 f16fe3031d..541c025e44 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 = "2.3.1" + String pipeline_version = "2.3.2" input { @@ -26,8 +26,8 @@ workflow ReblockGVCF { String gvcf_basename = basename(gvcf, gvcf_file_extension) # docker images - String gatk_docker_gcp = "us.gcr.io/broad-gatk/gatk:4.6.0.0" - String gatk_docker_azure = "terrapublic.azurecr.io/gatk:4.6.0.0" + String gatk_docker_gcp = "us.gcr.io/broad-gatk/gatk:4.6.1.0" + String gatk_docker_azure = "terrapublic.azurecr.io/gatk:4.6.1.0" String gatk_docker = if cloud_provider == "gcp" then gatk_docker_gcp else gatk_docker_azure # make sure either gcp or azr is supplied as cloud_provider input diff --git a/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.changelog.md b/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.changelog.md index 7531a4a61d..1c77ca0782 100644 --- a/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.changelog.md +++ b/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.changelog.md @@ -1,3 +1,8 @@ +# 3.2.3 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 3.2.2 2024-10-28 (Date of Last Commit) diff --git a/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl b/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl index 7dece64d75..edcd7893a4 100644 --- a/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl +++ b/pipelines/broad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.wdl @@ -45,7 +45,7 @@ import "../../../../../../tasks/broad/Utilities.wdl" as utils # WORKFLOW DEFINITION workflow ExomeGermlineSingleSample { - String pipeline_version = "3.2.2" + String pipeline_version = "3.2.3" input { @@ -68,8 +68,8 @@ workflow ExomeGermlineSingleSample { } # docker images - String gatk_docker_gcp = "us.gcr.io/broad-gatk/gatk:4.6.0.0" - String gatk_docker_azure = "terrapublic.azurecr.io/gatk:4.6.0.0" + String gatk_docker_gcp = "us.gcr.io/broad-gatk/gatk:4.6.1.0" + String gatk_docker_azure = "terrapublic.azurecr.io/gatk:4.6.1.0" String gatk_docker = if cloud_provider == "gcp" then gatk_docker_gcp else gatk_docker_azure # make sure either gcp or azr is supplied as cloud_provider input 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 a28c1d6a90..8e95e70d9e 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 @@ +# 1.1.2 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 1.1.1 2024-10-28 (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 d86df9539e..48d0be5283 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 = "1.1.1" + String pipeline_version = "1.1.2" References references = alignment_references.references diff --git a/pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.changelog.md b/pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.changelog.md index 91bf0f0f7f..1010a726d2 100644 --- a/pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.changelog.md +++ b/pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.changelog.md @@ -1,3 +1,8 @@ +# 3.3.3 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 3.3.2 2024-10-28 (Date of Last Commit) diff --git a/pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl b/pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl index 2635fca75c..b4507bc43b 100644 --- a/pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl +++ b/pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl @@ -40,7 +40,7 @@ import "../../../../../../structs/dna_seq/DNASeqStructs.wdl" workflow WholeGenomeGermlineSingleSample { - String pipeline_version = "3.3.2" + String pipeline_version = "3.3.3" input { diff --git a/pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.changelog.md b/pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.changelog.md index 3be5d2c9bb..c99cff07d7 100644 --- a/pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.changelog.md +++ b/pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.changelog.md @@ -1,3 +1,8 @@ +# 2.2.4 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 2.2.3 2024-10-28 (Date of Last Commit) diff --git a/pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.wdl b/pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.wdl index 3a1f0748a4..aaa38902fe 100644 --- a/pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.wdl +++ b/pipelines/broad/dna_seq/germline/variant_calling/VariantCalling.wdl @@ -9,7 +9,7 @@ import "../../../../../tasks/broad/DragenTasks.wdl" as DragenTasks workflow VariantCalling { - String pipeline_version = "2.2.3" + String pipeline_version = "2.2.4" input { @@ -40,8 +40,8 @@ workflow VariantCalling { } # docker images - String gatk_docker_gcp = "us.gcr.io/broad-gatk/gatk:4.6.0.0" - String gatk_docker_azure = "terrapublic.azurecr.io/gatk:4.6.0.0" + String gatk_docker_gcp = "us.gcr.io/broad-gatk/gatk:4.6.1.0" + String gatk_docker_azure = "terrapublic.azurecr.io/gatk:4.6.1.0" String gatk_docker = if cloud_provider == "gcp" then gatk_docker_gcp else gatk_docker_azure String gatk_1_3_docker_gcp = "us.gcr.io/broad-gotc-prod/gatk:1.3.0-4.2.6.1-1649964384" diff --git a/pipelines/broad/dna_seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.changelog.md b/pipelines/broad/dna_seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.changelog.md index bcb304a356..10f6e3d2b8 100644 --- a/pipelines/broad/dna_seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.changelog.md +++ b/pipelines/broad/dna_seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.changelog.md @@ -1,3 +1,8 @@ +# 1.0.23 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 1.0.22 2024-10-28 (Date of Last Commit) diff --git a/pipelines/broad/dna_seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.wdl b/pipelines/broad/dna_seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.wdl index 23c484698b..6a9940d884 100644 --- a/pipelines/broad/dna_seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.wdl +++ b/pipelines/broad/dna_seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.wdl @@ -43,7 +43,7 @@ workflow UltimaGenomicsWholeGenomeCramOnly { save_bam_file: "If true, then save intermeidate ouputs used by germline pipeline (such as the output BAM) otherwise they won't be kept as outputs." } - String pipeline_version = "1.0.22" + String pipeline_version = "1.0.23" References references = alignment_references.references diff --git a/pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.changelog.md b/pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.changelog.md index 7532807612..f7f046423d 100644 --- a/pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.changelog.md +++ b/pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.changelog.md @@ -1,3 +1,8 @@ +# 1.3.4 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 1.3.3 2024-09-06 (Date of Last Commit) diff --git a/pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl b/pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl index 80863f4d14..7cee55f51a 100644 --- a/pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl +++ b/pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/GDCWholeGenomeSomaticSingleSample.wdl @@ -533,7 +533,7 @@ task gatk_baserecalibrator { } runtime { - docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0" + docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0" memory: mem + " MiB" disks: "local-disk " + disk_space + " HDD" preemptible: preemptible @@ -580,7 +580,7 @@ task gatk_applybqsr { } runtime { - docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0" + docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0" memory: mem + " MiB" disks: "local-disk " + disk_space + " HDD" preemptible: preemptible @@ -623,7 +623,7 @@ task collect_insert_size_metrics { workflow GDCWholeGenomeSomaticSingleSample { - String pipeline_version = "1.3.3" + String pipeline_version = "1.3.4" input { File? input_cram diff --git a/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.changelog.md b/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.changelog.md index 9157f9faad..58b3562c74 100644 --- a/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.changelog.md +++ b/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.changelog.md @@ -1,3 +1,8 @@ +# 1.12.24 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 1.12.23 2024-10-28 (Date of Last Commit) diff --git a/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl b/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl index 5dfe13b1a5..6cee6c3eac 100644 --- a/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl +++ b/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.wdl @@ -21,7 +21,7 @@ import "../../../../tasks/broad/Qc.wdl" as Qc workflow IlluminaGenotypingArray { - String pipeline_version = "1.12.23" + String pipeline_version = "1.12.24" input { String sample_alias diff --git a/pipelines/broad/internal/arrays/imputation/BroadInternalImputation.changelog.md b/pipelines/broad/internal/arrays/imputation/BroadInternalImputation.changelog.md index 8d657fea1e..a0930046d7 100644 --- a/pipelines/broad/internal/arrays/imputation/BroadInternalImputation.changelog.md +++ b/pipelines/broad/internal/arrays/imputation/BroadInternalImputation.changelog.md @@ -1,3 +1,8 @@ +# 1.1.14 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 1.1.13 2024-09-06 (Date of Last Commit) diff --git a/pipelines/broad/internal/arrays/imputation/BroadInternalImputation.wdl b/pipelines/broad/internal/arrays/imputation/BroadInternalImputation.wdl index f1bb375e21..525ce85e00 100644 --- a/pipelines/broad/internal/arrays/imputation/BroadInternalImputation.wdl +++ b/pipelines/broad/internal/arrays/imputation/BroadInternalImputation.wdl @@ -9,7 +9,7 @@ workflow BroadInternalImputation { description: "Push outputs of Imputation.wdl to TDR dataset table ImputationOutputsTable and split out Imputation arrays into ImputationWideOutputsTable." allowNestedInputs: true } - String pipeline_version = "1.1.13" + String pipeline_version = "1.1.14" input { # inputs to wrapper task diff --git a/pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.changelog.md b/pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.changelog.md index c7967f1427..fca8ff1824 100644 --- a/pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.changelog.md +++ b/pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.changelog.md @@ -1,3 +1,8 @@ +# 1.1.14 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 1.1.13 2024-10-28 (Date of Last Commit) diff --git a/pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl b/pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl index a63ee8407c..4c2b46b30e 100644 --- a/pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl +++ b/pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.wdl @@ -9,7 +9,7 @@ workflow BroadInternalArrays { description: "Push outputs of Arrays.wdl to TDR dataset table ArraysOutputsTable." } - String pipeline_version = "1.1.13" + String pipeline_version = "1.1.14" input { # inputs to wrapper task 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 2365f13a21..1375589cbd 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 @@ +# 1.1.2 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 1.1.1 2024-10-28 (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 f9c9eaad7d..7c8ea24a44 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 = "1.1.1" + String pipeline_version = "1.1.2" input { diff --git a/pipelines/broad/internal/rna_seq/BroadInternalRNAWithUMIs.changelog.md b/pipelines/broad/internal/rna_seq/BroadInternalRNAWithUMIs.changelog.md index 34f0ff322f..6f287826d4 100644 --- a/pipelines/broad/internal/rna_seq/BroadInternalRNAWithUMIs.changelog.md +++ b/pipelines/broad/internal/rna_seq/BroadInternalRNAWithUMIs.changelog.md @@ -1,3 +1,8 @@ +# 1.0.36 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 1.0.35 2024-09-06 (Date of Last Commit) diff --git a/pipelines/broad/internal/rna_seq/BroadInternalRNAWithUMIs.wdl b/pipelines/broad/internal/rna_seq/BroadInternalRNAWithUMIs.wdl index aa13d1364d..66bc731283 100644 --- a/pipelines/broad/internal/rna_seq/BroadInternalRNAWithUMIs.wdl +++ b/pipelines/broad/internal/rna_seq/BroadInternalRNAWithUMIs.wdl @@ -7,7 +7,7 @@ import "../../../../tasks/broad/Utilities.wdl" as utils workflow BroadInternalRNAWithUMIs { - String pipeline_version = "1.0.35" + String pipeline_version = "1.0.36" input { # input needs to be either "hg19" or "hg38" diff --git a/pipelines/broad/reprocessing/exome/ExomeReprocessing.changelog.md b/pipelines/broad/reprocessing/exome/ExomeReprocessing.changelog.md index ae7def5e1f..a05a481e67 100644 --- a/pipelines/broad/reprocessing/exome/ExomeReprocessing.changelog.md +++ b/pipelines/broad/reprocessing/exome/ExomeReprocessing.changelog.md @@ -1,3 +1,8 @@ +# 3.3.3 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 3.3.2 2024-10-28 (Date of Last Commit) diff --git a/pipelines/broad/reprocessing/exome/ExomeReprocessing.wdl b/pipelines/broad/reprocessing/exome/ExomeReprocessing.wdl index bc824f0471..25e096c6a0 100644 --- a/pipelines/broad/reprocessing/exome/ExomeReprocessing.wdl +++ b/pipelines/broad/reprocessing/exome/ExomeReprocessing.wdl @@ -7,7 +7,7 @@ import "../../../../structs/dna_seq/DNASeqStructs.wdl" workflow ExomeReprocessing { - String pipeline_version = "3.3.2" + String pipeline_version = "3.3.3" input { File? input_cram diff --git a/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.changelog.md b/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.changelog.md index c262d4f6f6..b4f9d710c7 100644 --- a/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.changelog.md +++ b/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.changelog.md @@ -1,3 +1,8 @@ +# 3.3.3 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 3.3.2 2024-10-28 (Date of Last Commit) diff --git a/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.wdl b/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.wdl index 7ee18f74e9..f61df5874a 100644 --- a/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.wdl +++ b/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.wdl @@ -5,7 +5,7 @@ import "../../../../../tasks/broad/CopyFilesFromCloudToCloud.wdl" as Copy workflow ExternalExomeReprocessing { - String pipeline_version = "3.3.2" + String pipeline_version = "3.3.3" input { diff --git a/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.changelog.md b/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.changelog.md index a7a906a3a1..1aca6310da 100644 --- a/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.changelog.md +++ b/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.changelog.md @@ -1,3 +1,8 @@ +# 2.3.3 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 2.3.2 2024-10-28 (Date of Last Commit) diff --git a/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.wdl b/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.wdl index 7c709d915a..5962238e89 100644 --- a/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.wdl +++ b/pipelines/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.wdl @@ -6,7 +6,7 @@ import "../../../../../tasks/broad/CopyFilesFromCloudToCloud.wdl" as Copy workflow ExternalWholeGenomeReprocessing { - String pipeline_version = "2.3.2" + String pipeline_version = "2.3.3" input { File? input_cram diff --git a/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.changelog.md b/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.changelog.md index ef8ee3c4b9..97297884f4 100644 --- a/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.changelog.md +++ b/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.changelog.md @@ -1,3 +1,8 @@ +# 3.3.3 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 3.3.2 2024-10-28 (Date of Last Commit) diff --git a/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.wdl b/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.wdl index ef9d496ce7..99a01619a6 100644 --- a/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.wdl +++ b/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.wdl @@ -6,7 +6,7 @@ import "../../../../structs/dna_seq/DNASeqStructs.wdl" workflow WholeGenomeReprocessing { - String pipeline_version = "3.3.2" + String pipeline_version = "3.3.3" input { File? input_cram diff --git a/pipelines/broad/rna_seq/RNAWithUMIsPipeline.changelog.md b/pipelines/broad/rna_seq/RNAWithUMIsPipeline.changelog.md index ea9ddaa829..cee789a0f9 100644 --- a/pipelines/broad/rna_seq/RNAWithUMIsPipeline.changelog.md +++ b/pipelines/broad/rna_seq/RNAWithUMIsPipeline.changelog.md @@ -1,3 +1,8 @@ +# 1.0.18 +2024-11-04 (Date of Last Commit) + +* Updated to GATK version 4.6.1.0 + # 1.0.17 2024-09-06 (Date of Last Commit) diff --git a/pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl b/pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl index cfc728baa0..b4904a8889 100644 --- a/pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl +++ b/pipelines/broad/rna_seq/RNAWithUMIsPipeline.wdl @@ -20,7 +20,7 @@ import "../../../tasks/broad/RNAWithUMIsTasks.wdl" as tasks workflow RNAWithUMIsPipeline { - String pipeline_version = "1.0.17" + String pipeline_version = "1.0.18" input { File? bam diff --git a/scripts/BuildAFComparisonTable.wdl b/scripts/BuildAFComparisonTable.wdl index 1a0b3b81bb..44dac9bc3e 100644 --- a/scripts/BuildAFComparisonTable.wdl +++ b/scripts/BuildAFComparisonTable.wdl @@ -117,7 +117,7 @@ task AnnotateWithAF_t { >>> runtime { - docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0" + docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0" disks: "local-disk " + disk_size + " HDD" memory: mem + " GB" # some of the gnomad vcfs are like 38 gigs so maybe need more ? } @@ -145,7 +145,7 @@ task GatherVCFsCloud { >>> runtime { - docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0" + docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0" disks: "local-disk " + disk_size + " HDD" memory: "16 GB" } @@ -169,7 +169,7 @@ task MakeSitesOnlyVcf { >>> runtime { - docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0" + docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0" disks: "local-disk " + disk_size + " HDD" memory: "16 GB" } @@ -224,7 +224,7 @@ task VariantsToTable { >>> runtime { - docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0" + docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0" disks: "local-disk " + disk_size + " HDD" memory: "16 GB" } @@ -280,7 +280,7 @@ task RemoveSymbolicAlleles { File output_vcf_index = "~{output_basename}.vcf.gz.tbi" } runtime { - docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0" + docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0" disks: "local-disk " + disk_size + " HDD" memory: "4 GB" } diff --git a/scripts/RemoveBadSitesByID.wdl b/scripts/RemoveBadSitesByID.wdl index 378c26e31c..9299d7e96a 100644 --- a/scripts/RemoveBadSitesByID.wdl +++ b/scripts/RemoveBadSitesByID.wdl @@ -129,7 +129,7 @@ task SplitX { >>> runtime { - docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0" + docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0" disks: "local-disk " + disk_size + " HDD" memory: "16 GB" } @@ -215,7 +215,7 @@ task RemoveBadSitesFromVcf { >>> runtime { - docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0" + docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0" disks: "local-disk 100 HDD" memory: "16 GB" } diff --git a/tasks/broad/CheckContaminationSomatic.wdl b/tasks/broad/CheckContaminationSomatic.wdl index dd70628962..5cc8715e91 100644 --- a/tasks/broad/CheckContaminationSomatic.wdl +++ b/tasks/broad/CheckContaminationSomatic.wdl @@ -14,7 +14,7 @@ task CalculateSomaticContamination { File contamination_vcf_index # runtime - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.2.4.1" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" File? gatk_override Int? additional_disk Int memory_mb = 3000 diff --git a/tasks/broad/DragenTasks.wdl b/tasks/broad/DragenTasks.wdl index 57146b7a02..11aae23dbb 100644 --- a/tasks/broad/DragenTasks.wdl +++ b/tasks/broad/DragenTasks.wdl @@ -25,7 +25,7 @@ task CalibrateDragstrModel { File alignment ## can handle cram or bam. File alignment_index #Setting default docker value for workflows that haven't yet been azurized. - String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int preemptible_tries = 3 Int threads = 4 Int? memory_mb diff --git a/tasks/broad/GermlineVariantDiscovery.wdl b/tasks/broad/GermlineVariantDiscovery.wdl index 13882cb6df..7538290e08 100644 --- a/tasks/broad/GermlineVariantDiscovery.wdl +++ b/tasks/broad/GermlineVariantDiscovery.wdl @@ -99,7 +99,7 @@ task HaplotypeCaller_GATK4_VCF { Boolean use_spanning_event_genotyping = true File? dragstr_model #Setting default docker value for workflows that haven't yet been azurized. - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int memory_multiplier = 1 } @@ -261,7 +261,7 @@ task HardFilterVcf { String vcf_basename File interval_list Int preemptible_tries - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" } Int disk_size = ceil(2 * size(input_vcf, "GiB")) + 20 @@ -337,7 +337,7 @@ task CNNScoreVariants { File ref_fasta_index File ref_dict Int preemptible_tries - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" } Int disk_size = ceil(size(bamout, "GiB") + size(ref_fasta, "GiB") + (size(input_vcf, "GiB") * 2)) @@ -394,7 +394,7 @@ task FilterVariantTranches { File dbsnp_resource_vcf_index String info_key Int preemptible_tries - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" } Int disk_size = ceil(size(hapmap_resource_vcf, "GiB") + diff --git a/tasks/broad/IlluminaGenotypingArrayTasks.wdl b/tasks/broad/IlluminaGenotypingArrayTasks.wdl index 49971de93e..ab362104a9 100644 --- a/tasks/broad/IlluminaGenotypingArrayTasks.wdl +++ b/tasks/broad/IlluminaGenotypingArrayTasks.wdl @@ -404,7 +404,7 @@ task SelectVariants { >>> runtime { - docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0" + docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0" bootDiskSizeGb: 15 disks: "local-disk " + disk_size + " HDD" memory: "3500 MiB" @@ -441,7 +441,7 @@ task SelectIndels { >>> runtime { - docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0" + docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0" bootDiskSizeGb: 15 disks: "local-disk " + disk_size + " HDD" memory: "3500 MiB" @@ -577,7 +577,7 @@ task SubsetArrayVCF { } runtime { - docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0" + docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0" bootDiskSizeGb: 15 disks: "local-disk " + disk_size + " HDD" memory: "3500 MiB" @@ -676,7 +676,7 @@ task ValidateVariants { >>> runtime { - docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0" + docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0" bootDiskSizeGb: 15 disks: "local-disk " + disk_size + " HDD" memory: "3500 MiB" diff --git a/tasks/broad/ImputationTasks.wdl b/tasks/broad/ImputationTasks.wdl index 02bdb2e603..793ae119b2 100644 --- a/tasks/broad/ImputationTasks.wdl +++ b/tasks/broad/ImputationTasks.wdl @@ -65,7 +65,7 @@ task GenerateChunk { Int disk_size_gb = ceil(2*size(vcf, "GiB")) + 50 # not sure how big the disk size needs to be since we aren't downloading the entire VCF here Int cpu = 1 Int memory_mb = 8000 - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" } Int command_mem = memory_mb - 1000 Int max_heap = memory_mb - 500 @@ -112,7 +112,7 @@ task CountVariantsInChunks { File panel_vcf File panel_vcf_index - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int cpu = 1 Int memory_mb = 4000 Int disk_size_gb = 2 * ceil(size([vcf, vcf_index, panel_vcf, panel_vcf_index], "GiB")) + 20 @@ -266,7 +266,7 @@ task GatherVcfs { Array[File] input_vcfs String output_vcf_basename - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int cpu = 1 Int memory_mb = 16000 Int disk_size_gb = ceil(3*size(input_vcfs, "GiB")) @@ -336,7 +336,7 @@ task UpdateHeader { String basename Int disk_size_gb = ceil(4*(size(vcf, "GiB") + size(vcf_index, "GiB"))) + 20 - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int cpu = 1 Int memory_mb = 8000 } @@ -372,7 +372,7 @@ task RemoveSymbolicAlleles { String output_basename Int disk_size_gb = ceil(3*(size(original_vcf, "GiB") + size(original_vcf_index, "GiB"))) - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int cpu = 1 Int memory_mb = 4000 } @@ -659,7 +659,7 @@ task SubsetVcfToRegion { Int disk_size_gb = ceil(2*size(vcf, "GiB")) + 50 # not sure how big the disk size needs to be since we aren't downloading the entire VCF here Int cpu = 1 Int memory_mb = 8000 - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" } Int command_mem = memory_mb - 1000 Int max_heap = memory_mb - 500 @@ -754,7 +754,7 @@ task SelectVariantsByIds { File ids String basename - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int cpu = 1 Int memory_mb = 16000 Int disk_size_gb = ceil(1.2*size(vcf, "GiB")) + 100 @@ -820,7 +820,7 @@ task InterleaveVariants { Array[File] vcfs String basename - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int cpu = 1 Int memory_mb = 16000 Int disk_size_gb = ceil(3.2*size(vcfs, "GiB")) + 100 diff --git a/tasks/broad/JointGenotypingTasks.wdl b/tasks/broad/JointGenotypingTasks.wdl index a38fdfc614..9e6378a9b5 100644 --- a/tasks/broad/JointGenotypingTasks.wdl +++ b/tasks/broad/JointGenotypingTasks.wdl @@ -51,7 +51,7 @@ task SplitIntervalList { Int machine_mem_mb = 3750 String scatter_mode = "BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW" String? extra_args - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" } parameter_meta { @@ -94,7 +94,7 @@ task ImportGVCFs { Int machine_mem_mb = 30000 Int batch_size - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" } command <<< @@ -159,7 +159,7 @@ task GenotypeGVCFs { Int machine_mem_mb = 26000 # This is needed for gVCFs generated with GATK3 HaplotypeCaller Boolean allow_old_rms_mapping_quality_annotation_data = false - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" } parameter_meta { @@ -216,7 +216,7 @@ task GnarlyGenotyper { String dbsnp_vcf Boolean make_annotation_db = false - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int machine_mem_mb = 26000 Int disk_size_gb = ceil(size(workspace_tar, "GiB") + size(ref_fasta, "GiB") + size(dbsnp_vcf, "GiB") * 3) } @@ -277,7 +277,7 @@ task HardFilterAndMakeSitesOnlyVcf { Int disk_size_gb Int machine_mem_mb = 3750 - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" } command <<< @@ -339,7 +339,7 @@ task IndelsVariantRecalibrator { Int disk_size_gb Int machine_mem_mb = 26000 - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" } command <<< @@ -404,7 +404,7 @@ task SNPsVariantRecalibratorCreateModel { Int disk_size_gb Int machine_mem_mb = 104000 - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" } command <<< @@ -468,7 +468,7 @@ task SNPsVariantRecalibrator { Int max_gaussians = 6 Int disk_size_gb - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int? machine_mem_mb } @@ -533,7 +533,7 @@ task GatherTranches { String mode Int disk_size_gb Int machine_mem_mb = 7500 - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" } parameter_meta { @@ -607,7 +607,7 @@ task ApplyRecalibration { Boolean use_allele_specific_annotations Int disk_size_gb Int machine_mem_mb = 7000 - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" } command <<< @@ -658,7 +658,7 @@ task GatherVcfs { String output_vcf_name Int disk_size_gb Int machine_mem_mb = 7000 - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" } parameter_meta { @@ -706,7 +706,7 @@ task SelectFingerprintSiteVariants { String base_output_name Int disk_size_gb Int machine_mem_mb = 7500 - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" } parameter_meta { @@ -759,7 +759,7 @@ task CollectVariantCallingMetrics { File ref_dict Int disk_size_gb Int machine_mem_mb = 7500 - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" } command <<< @@ -798,7 +798,7 @@ task GatherVariantCallingMetrics { String output_prefix Int disk_size_gb Int machine_mem_mb = 3000 - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" } parameter_meta { @@ -879,7 +879,7 @@ task CrossCheckFingerprint { String output_base_name Boolean scattered = false Array[String] expected_inconclusive_samples = [] - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int? machine_mem_mb Int disk = 100 } @@ -1000,7 +1000,7 @@ task GetFingerprintingIntervalIndices { input { Array[File] unpadded_intervals File haplotype_database - String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int disk_size_gb = 10 Int machine_mem_mb = 3750 } @@ -1114,7 +1114,7 @@ task CalculateAverageAnnotations { File vcf Array[String] annotations_to_divide = ["ASSEMBLED_HAPS", "FILTERED_HAPS", "TREE_SCORE"] - String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int disk_size_gb = ceil(size(vcf, "GB") + 50) Int memory_mb = 12000 Int preemptible = 3 diff --git a/tasks/broad/RNAWithUMIsTasks.wdl b/tasks/broad/RNAWithUMIsTasks.wdl index 32cef74b85..7997da9274 100644 --- a/tasks/broad/RNAWithUMIsTasks.wdl +++ b/tasks/broad/RNAWithUMIsTasks.wdl @@ -278,7 +278,7 @@ task GetSampleName { input { File bam - String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int cpu = 1 Int memory_mb = 1000 Int disk_size_gb = ceil(2.0 * size(bam, "GiB")) + 10 @@ -852,7 +852,7 @@ task CalculateContamination { File population_vcf File population_vcf_index # runtime - String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int cpu = 1 Int memory_mb = 8192 Int disk_size_gb = 256 @@ -965,7 +965,7 @@ task TransferReadTags { File aligned_bam File ubam String output_basename - String docker = "us.gcr.io/broad-gatk/gatk:4.4.0.0" + String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int memory_mb = 16000 Int disk_size_gb = ceil(2 * size(aligned_bam, "GiB")) + ceil(2 * size(ubam, "GiB")) + 128 } @@ -994,7 +994,7 @@ task PostprocessTranscriptomeForRSEM { String prefix File input_bam # the input must be queryname sorted Int disk_size_gb = ceil(3*size(input_bam,"GiB")) + 128 - String docker = "us.gcr.io/broad-gatk/gatk:4.2.6.0" + String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int memory_mb = 16000 } @@ -1019,7 +1019,7 @@ task PostprocessTranscriptomeForRSEM { task CreateEmptyFile { input { Int disk_size_gb = 128 - String docker = "us.gcr.io/broad-gatk/gatk:4.2.6.0" + String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int memory_mb = 4096 } diff --git a/tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl b/tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl index 98af0810f5..431362da87 100644 --- a/tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl +++ b/tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl @@ -326,7 +326,7 @@ task HardThresholdVCF { String output_basename String score_key Int disk_size - String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" } command <<< @@ -384,7 +384,7 @@ task AnnotateSampleVCF { File input_vcf_index String output_basename Int disk_size = ceil(size(input_vcf, "GB") * 2) + 50 - String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" File ref_fasta File ref_fasta_index File ref_dict diff --git a/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl b/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl index 19831dbaa2..739b44202c 100644 --- a/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl +++ b/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl @@ -56,7 +56,7 @@ task SplitCram { String base_file_name Int reads_per_file - String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int disk_size_gb = ceil(3 * size(input_cram_bam, "GiB") + 20) Int cpu = 1 Int memory_gb = 10 @@ -269,7 +269,7 @@ task MarkDuplicatesSpark { Array[File] input_bams String output_bam_basename Boolean save_bam_file - String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int disk_size_gb Int cpu = 32 Int memory_mb = if 4 * ceil(size(input_bams, "MB")) / 4000 > 600000 then 300000 else 208000 @@ -319,7 +319,7 @@ task ExtractSampleNameFlowOrder{ File input_bam References references - String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int disk_size_gb = ceil(size(input_bam, "GB") + size(references.ref_fasta, "GB") + 20) Int cpu = 1 Int memory_mb = 2000 @@ -480,7 +480,7 @@ task HaplotypeCaller { Boolean native_sw = false String? contamination_extra_args - String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int disk_size_gb = ceil((size(input_bam_list, "GB")) + size(references.ref_fasta, "GB") + size(references.ref_fasta_index, "GB") + size(references.ref_dict, "GB") + 60) Int cpu = 2 Int memory_mb = 12000 @@ -591,7 +591,7 @@ task ConvertGVCFtoVCF { String output_vcf_name References references - String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int disk_size_gb = ceil(2 * size(input_gvcf, "GB") + size(references.ref_fasta, "GB") + size(input_gvcf_index, "GB") + 20) Int cpu = 1 Int memory_mb = 12000 @@ -947,7 +947,7 @@ task AnnotateVCF { String flow_order String final_vcf_base_name - String docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0" + String docker = "us.gcr.io/broad-gatk/gatk:4.6.1.0" Int disk_size_gb = ceil(2 * size(input_vcf, "GB") + size(references.ref_fasta, "GB") + size(reference_dbsnp, "GB") + 20) Int cpu = 1 Int memory_mb = 15000 diff --git a/verification/VerifyNA12878.wdl b/verification/VerifyNA12878.wdl index b7ecfe1dbe..3d5720df4d 100644 --- a/verification/VerifyNA12878.wdl +++ b/verification/VerifyNA12878.wdl @@ -86,7 +86,7 @@ task RunValidation { } runtime { - docker: "us.gcr.io/broad-gatk/gatk:4.6.0.0" + docker: "us.gcr.io/broad-gatk/gatk:4.6.1.0" memory: machine_mem + " MiB" disks: "local-disk " + select_first([disk_space, 100]) + if use_ssd then " SSD" else " HDD" diff --git a/verification/VerifyUltimaGenomicsJointGenotyping.wdl b/verification/VerifyUltimaGenomicsJointGenotyping.wdl index aa0c6ded02..250f5a8f1f 100644 --- a/verification/VerifyUltimaGenomicsJointGenotyping.wdl +++ b/verification/VerifyUltimaGenomicsJointGenotyping.wdl @@ -31,6 +31,17 @@ workflow VerifyJointGenotyping { test_gvcf = test_vcfs[idx], truth_gvcf = truth_vcfs[idx] } + + call VerifyTasks.CompareVCFsVerbosely as CompareFilteredVcfsVerbosely { + input: + actual = test_vcfs[idx], + expected = truth_vcfs[idx], + actual_index = test_vcf_indexes[idx], + expected_index = truth_vcf_indexes[idx], + extra_args = " --ignore-attribute AVERAGE_TREE_SCORE --ignore-attribute CALIBRATION_SENSITIVITY " + + "--ignore-attribute TREE_SCORE --ignore-attribute SCORE --ignore-filters --ignore-attribute AS_FilterStatus " + + "--ignore-attribute ExcessHet --ignore-star-attributes --allow-nan-mismatch --ignore-attribute END" + } } call MetricsVerification.VerifyMetrics { diff --git a/verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl b/verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl index 28a7924209..ec2f2bcbea 100755 --- a/verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl +++ b/verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl @@ -24,6 +24,8 @@ workflow VerifyUltimaGenomicsWholeGenomeGermline { File test_gvcf File truth_gvcf + File truth_gvcf_index + File test_gvcf_index String sample_name @@ -109,6 +111,17 @@ workflow VerifyUltimaGenomicsWholeGenomeGermline { patternForLinesToExcludeFromComparison = "^##" } + call Tasks.CompareVCFsVerbosely as CompareGVcfsVerbosely { + input: + actual = test_gvcf, + expected = truth_gvcf, + actual_index = test_gvcf_index, + expected_index = truth_gvcf_index, + extra_args = " --ignore-attribute AVERAGE_TREE_SCORE --ignore-attribute CALIBRATION_SENSITIVITY " + + "--ignore-attribute TREE_SCORE --ignore-attribute SCORE --ignore-filters --ignore-attribute AS_FilterStatus " + + "--ignore-attribute ExcessHet --ignore-star-attributes --allow-nan-mismatch --ignore-attribute END" + } + call VerifyNA12878.VerifyNA12878 { input: vcf_files = [test_filtered_vcf, truth_filtered_vcf], diff --git a/verification/test-wdls/TestBroadInternalUltimaGenomics.wdl b/verification/test-wdls/TestBroadInternalUltimaGenomics.wdl index 8028244d9e..22ae4bc7aa 100644 --- a/verification/test-wdls/TestBroadInternalUltimaGenomics.wdl +++ b/verification/test-wdls/TestBroadInternalUltimaGenomics.wdl @@ -173,6 +173,12 @@ workflow TestBroadInternalUltimaGenomics { results_path = results_path, truth_path = truth_path } + call Utilities.GetValidationInputs as GetGvcfIndex { + input: + input_file = BroadInternalUltimaGenomics.output_gvcf_index, + results_path = results_path, + truth_path = truth_path + } call VerifyUltimaGenomicsWholeGenomeGermline.VerifyUltimaGenomicsWholeGenomeGermline as Verify { input: @@ -190,6 +196,8 @@ workflow TestBroadInternalUltimaGenomics { test_filtered_vcf_index = GetFilteredVcfIndex.results_file, truth_gvcf = GetGvcf.truth_file, test_gvcf = GetGvcf.results_file, + truth_gvcf_index = GetGvcfIndex.truth_file, + test_gvcf_index = GetGvcfIndex.results_file, sample_name = BroadInternalUltimaGenomics.sample_name, done = CopyToTestResults.done } diff --git a/verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl b/verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl index fbbca9cc29..9e1af52645 100644 --- a/verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl +++ b/verification/test-wdls/TestUltimaGenomicsWholeGenomeGermline.wdl @@ -156,6 +156,13 @@ workflow TestUltimaGenomicsWholeGenomeGermline { truth_path = truth_path } + call Utilities.GetValidationInputs as GetGvcfIndex { + input: + input_file = UltimaGenomicsWholeGenomeGermline.output_gvcf_index, + results_path = results_path, + truth_path = truth_path + } + call VerifyUltimaGenomicsWholeGenomeGermline.VerifyUltimaGenomicsWholeGenomeGermline as Verify { input: truth_metrics = GetMetrics.truth_files, @@ -172,6 +179,8 @@ workflow TestUltimaGenomicsWholeGenomeGermline { test_filtered_vcf_index = GetFilteredVcfIndex.results_file, truth_gvcf = GetGvcf.truth_file, test_gvcf = GetGvcf.results_file, + truth_gvcf_index = GetGvcfIndex.truth_file, + test_gvcf_index = GetGvcfIndex.results_file, sample_name = UltimaGenomicsWholeGenomeGermline.sample_name, done = CopyToTestResults.done }