broadinstitute · nikellepetrillo · Sep 10, 2024 · Sep 10, 2024
diff --git a/pipeline_versions.txt b/pipeline_versions.txt
@@ -11,32 +11,32 @@ scATAC 1.3.2 2023-08-03
 BuildIndices 3.0.0 2023-12-06 
 SlideSeq 3.4.0 2024-08-06 
 BuildCembaReferences 1.0.0 2020-11-15 
-CEMBA 1.1.6 2023-12-18 
-GDCWholeGenomeSomaticSingleSample 1.3.2 2024-08-02  
-UltimaGenomicsWholeGenomeCramOnly 1.0.20 2024-08-02 
-JointGenotypingByChromosomePartOne 1.4.12 2023-12-18 
-JointGenotypingByChromosomePartTwo 1.4.11 2023-12-18 
-UltimaGenomicsJointGenotyping 1.1.7 2023-12-18 
-JointGenotyping 1.6.10 2023-12-18 
-ReblockGVCF 2.2.1 2024-06-12 
-VariantCalling 2.2.1 2024-06-12 
-WholeGenomeGermlineSingleSample 3.2.1 2024-06-12 
-UltimaGenomicsWholeGenomeGermline 1.0.20 2024-08-02 
-ExomeGermlineSingleSample 3.1.22 2024-06-12 
-ValidateChip 1.16.5 2024-08-02 
-Arrays 2.6.27 2024-08-02 
-Imputation 1.1.13 2024-05-21 
+CEMBA 1.1.7 2024-09-06 
+GDCWholeGenomeSomaticSingleSample 1.3.3 2024-09-06 
+UltimaGenomicsWholeGenomeCramOnly 1.0.21 2024-09-06 
+JointGenotypingByChromosomePartOne 1.5.0 2024-09-06 
+JointGenotypingByChromosomePartTwo 1.5.0 2024-09-06 
+UltimaGenomicsJointGenotyping 1.2.0 2024-09-06 
+JointGenotyping 1.7.0 2024-09-06 
+ReblockGVCF 2.3.0 2024-09-06 
+VariantCalling 2.2.2 2024-09-06 
+WholeGenomeGermlineSingleSample 3.3.0 2024-09-06 
+UltimaGenomicsWholeGenomeGermline 1.1.0 2024-09-06 
+ExomeGermlineSingleSample 3.2.0 2024-09-06 
+ValidateChip 1.16.6 2024-09-06 
+Arrays 2.6.28 2024-09-06 
+Imputation 1.1.14 2024-09-06 
 MultiSampleArrays 1.6.2 2024-08-02 
-BroadInternalUltimaGenomics 1.0.21 2024-08-02 
-BroadInternalArrays 1.1.11 2024-08-02 
-BroadInternalImputation 1.1.12 2024-08-02 
-BroadInternalRNAWithUMIs 1.0.33 2024-08-02 
+BroadInternalUltimaGenomics 1.1.0 2024-09-06 
+BroadInternalArrays 1.1.12 2024-09-06 
+BroadInternalImputation 1.1.13 2024-09-06 
+BroadInternalRNAWithUMIs 1.0.34 2024-09-06 
 CramToUnmappedBams 1.1.3 2024-08-02 
-ExternalWholeGenomeReprocessing 2.2.2 2024-08-02 
-ExternalExomeReprocessing 3.2.2 2024-08-02 
-WholeGenomeReprocessing 3.2.2 2024-08-02 
-ExomeReprocessing 3.2.2 2024-08-02 
-IlluminaGenotypingArray 1.12.21 2024-08-02 
-CheckFingerprint 1.0.20 2024-08-02 
-AnnotationFiltration 1.2.5 2023-12-18 
-RNAWithUMIsPipeline 1.0.16 2023-12-18 
+ExternalWholeGenomeReprocessing 2.3.0 2024-09-06 
+ExternalExomeReprocessing 3.3.0 2024-09-06 
+WholeGenomeReprocessing 3.3.0 2024-09-06 
+ExomeReprocessing 3.3.0 2024-09-06 
+IlluminaGenotypingArray 1.12.22 2024-09-06 
+CheckFingerprint 1.0.21 2024-09-06 
+AnnotationFiltration 1.2.6 2024-09-06 
+RNAWithUMIsPipeline 1.0.17 2024-09-06 
diff --git a/pipelines/broad/annotation_filtration/AnnotationFiltration.changelog.md b/pipelines/broad/annotation_filtration/AnnotationFiltration.changelog.md
@@ -1,3 +1,8 @@
+# 1.2.6
+2024-09-06 (Date of Last Commit)
+
+* Updated to GATK version 4.6.0.0
+
 # 1.2.5
 2023-12-18 (Date of Last Commit)
 

diff --git 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 = "1.2.5"
+ String pipeline_version = "1.2.6"
 
  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:4.5.0.0"
+ String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
  File? custom_data_source_tar_gz
  }
 

diff --git a/pipelines/broad/arrays/imputation/Imputation.changelog.md b/pipelines/broad/arrays/imputation/Imputation.changelog.md
@@ -1,9 +1,13 @@
+# 1.1.14
+2024-09-06 (Date of Last Commit)
+
+* Updated to GATK version 4.6.0.0
+
 # 1.1.13
 2024-05-21 (Date of Last Commit)
 
 * Updated GermlineVariantDiscovery, BamProcessing, DragenTasks, Qc, and Utilities tasks to allow multi-cloud dockers. This change does not affect this pipeline.
 
-
 # 1.1.12
 2023-12-18 (Date of Last Commit)
 

diff --git 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 = "1.1.13"
+ String pipeline_version = "1.1.14"
 
  input {
  Int chunkLength = 25000000

diff --git a/pipelines/broad/arrays/single_sample/Arrays.changelog.md b/pipelines/broad/arrays/single_sample/Arrays.changelog.md
@@ -1,3 +1,8 @@
+# 2.6.28
+2024-09-06 (Date of Last Commit)
+
+* Updated to GATK version 4.6.0.0
+
 # 2.6.27
 2024-08-02 (Date of Last Commit)
 

diff --git 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 = "2.6.27"
+ String pipeline_version = "2.6.28"
 
  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
@@ -1,3 +1,8 @@
+# 1.16.6
+2024-09-06 (Date of Last Commit)
+
+* Updated to GATK version 4.6.0.0
+
 # 1.16.5
 2024-08-02 (Date of Last Commit)
 

diff --git 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 = "1.16.5"
+ String pipeline_version = "1.16.6"
 
  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
@@ -1,3 +1,9 @@
+# 1.7.0
+2024-09-06 (Date of Last Commit)
+
+* Updated to GATK version 4.6.0.0
+* Updated how no-calls are represented in the output VCFs (0/0 -> ./.) which also changes some annotations in the VCF
+
 # 1.6.10
 2023-12-18 (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
@@ -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 = "1.6.10"
+ String pipeline_version = "1.7.0"
 
  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:4.5.0.0"
+ gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
  }
  } 
  if (!run_vets) {

diff --git a/...line/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.changelog.md b/...line/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.changelog.md
@@ -1,3 +1,9 @@
+# 1.2.0
+2024-09-06 (Date of Last Commit)
+
+* Updated to GATK version 4.6.0.0
+* Updated how no-calls are represented in the output VCFs (0/0 -> ./.) which also changes some annotations in the VCF
+
 # 1.1.7
 2023-12-18 (Date of Last Commit)
 

diff --git a/.../broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.wdl b/.../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 = "1.1.7"
+ String pipeline_version = "1.2.0"
 
  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:4.5.0.0"
+ gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
  }
 
  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:4.5.0.0"
+ gatk_docker = "us.gcr.io/broad-gatk/gatk:4.6.0.0"
  }
 
  call FilteringThreshold.ExtractOptimizeSingleSample as FindFilteringThresholdAndFilter {

diff --git a/.../joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md b/.../joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md
@@ -1,3 +1,9 @@
+# 1.5.0
+2024-09-06 (Date of Last Commit)
+
+* Updated to GATK version 4.6.0.0 
+* Updated how no-calls are represented in the output VCFs (0/0 -> ./.) which also changes some annotations in the VCF
+
 # 1.4.12
 2023-12-18 (Date of Last Commit)
 

diff --git a/...ad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl b/...ad/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 = "1.4.12"
+ String pipeline_version = "1.5.0"
 
  input {
  File unpadded_intervals_file

diff --git a/.../joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.changelog.md b/.../joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.changelog.md
@@ -1,3 +1,9 @@
+# 1.5.0
+2024-09-06 (Date of Last Commit)
+
+* Updated to GATK version 4.6.0.0
+* Updated how no-calls are represented in the output VCFs (0/0 -> ./.) which also changes some annotations in the VCF
+
 # 1.4.11
 2023-12-18 (Date of Last Commit)
 

diff --git a/...ad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl b/...ad/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 = "1.4.11"
+ String pipeline_version = "1.5.0"
 
  input {
  String callset_name

diff --git a/...nes/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.changelog.md b/...nes/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.changelog.md
@@ -1,3 +1,8 @@
+# 2.3.0
+2024-09-06 (Date of Last Commit)
+
+* Updated to GATK version 4.6.0.0. Some expected minor differences around low quality sites (GQ0 genotypes or no-calls)
+
 # 2.2.1
 2024-06-12 (Date of Last Commit)
 
@@ -6,7 +11,7 @@
 # 2.2.0
 2024-07-09 (Date of Last Commit)
 
-* Updated ReblockGVCF.wdl to run in Azure. cloud_provider is a new, required input. 
+* Updated ReblockGVCF.wdl to run in Azure. cloud_provider is a new, required input 
 
 # 2.1.13
 2024-07-01 (Date of Last Commit)
@@ -16,12 +21,12 @@
 # 2.1.12
 2024-03-26 (Date of Last Commit)
 
-* ValidateVcfs requires less memory when run without interval list. This is useful for WGS samples that were previously running out of memory.
+* ValidateVcfs requires less memory when run without interval list. This is useful for WGS samples that were previously running out of memory
 
 # 2.1.11
 2023-12-18 (Date of Last Commit)
 
-* Updated to GATK version 4.5.0.0. Header documentation change for RAW_GT_COUNT annotation.
+* Updated to GATK version 4.5.0.0. Header documentation change for RAW_GT_COUNT annotation
 
 # 2.1.10
 2023-12-14 (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
@@ -6,7 +6,7 @@ import "../../../../../../tasks/broad/Utilities.wdl" as utils
 
 workflow ReblockGVCF {
 
- String pipeline_version = "2.2.1"
+ String pipeline_version = "2.3.0"
 
 
  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:4.5.0.0"
- String gatk_docker_azure = "dsppipelinedev.azurecr.io/gatk_reduced_layers:1.0.0"
+ 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 = 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/...oad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.changelog.md b/...oad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.changelog.md
@@ -1,3 +1,9 @@
+# 3.2.0
+2024-09-06 (Date of Last Commit)
+
+* Updated to GATK version 4.6.0.0
+* Updated version drops some low quality sites from VCFs; if reblocking is enabled, the DP annotation in some ref blocks will change due to the change in HaplotypeCaller
+
 # 3.1.22
 2024-06-12 (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
@@ -45,7 +45,7 @@ import "../../../../../../tasks/broad/Utilities.wdl" as utils
 # WORKFLOW DEFINITION
 workflow ExomeGermlineSingleSample {
 
- String pipeline_version = "3.1.22"
+ String pipeline_version = "3.2.0"
 
 
  input {
@@ -68,8 +68,8 @@ workflow ExomeGermlineSingleSample {
  }
 
  # docker images
- String gatk_docker_gcp = "us.gcr.io/broad-gatk/gatk:4.5.0.0"
- String gatk_docker_azure = "dsppipelinedev.azurecr.io/gatk_reduced_layers:1.0.0"
+ 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 = 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/...seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.changelog.md b/...seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.changelog.md
@@ -1,3 +1,9 @@
+# 1.1.0
+2024-09-06 (Date of Last Commit)
+
+* Updated to GATK version 4.6.0.0
+* Minor changes to the output VCF at some sites due to the changes in HaplotyperCaller
+
 # 1.0.20
 2024-08-02 (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
@@ -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 = "1.0.20"
+ String pipeline_version = "1.1.0"
 
 
  References references = alignment_references.references

diff --git a/...dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.changelog.md b/...dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.changelog.md
@@ -1,3 +1,9 @@
+# 3.3.0
+2024-09-06 (Date of Last Commit)
+
+* Updated to GATK version 4.6.0.0
+* Updated version drops some low quality sites from VCFs; if reblocking is enabled, the DP annotation in some ref blocks will change due to the change in HaplotypeCaller
+
 # 3.2.1
 2024-06-12 (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
@@ -40,7 +40,7 @@ import "../../../../../../structs/dna_seq/DNASeqStructs.wdl"
 workflow WholeGenomeGermlineSingleSample {
 
 
- String pipeline_version = "3.2.1"
+ String pipeline_version = "3.3.0"
 
 
  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
@@ -1,3 +1,8 @@
+# 2.2.2
+2024-09-06 (Date of Last Commit)
+
+* Updated to GATK version 4.6.0.0
+
 # 2.2.1
 2024-06-12 (Date of Last Commit)