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 <[email protected]>
broadinstitute · Nov 5, 2024 · d7c2443 · d7c2443
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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/...line/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.changelog.md b/...line/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/.../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 = "1.2.1"
+  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/.../joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md b/.../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/...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 = "1.5.1"
+  String pipeline_version = "1.5.2"
 
   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 +1,8 @@
+# 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/...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 = "1.5.1"
+  String pipeline_version = "1.5.2"
 
   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 @@
+# 2.3.2
+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
@@ -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/...oad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.changelog.md b/...oad/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
@@ -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/...seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.changelog.md b/...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
@@ -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/...dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.changelog.md b/...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
@@ -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
@@ -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
@@ -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/..._seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.changelog.md b/..._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
@@ -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
-Original file line number
+Diff line change
@@ Expand Up / @@ -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 {
@@ Expand Down @@