Merge branch 'develop' into aa-starsolo-one

broadinstitute · Mar 18, 2024 · b6eb327 · b6eb327
2 parents b0ba813 + 47fb3c3
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diff --git a/README.md b/README.md
@@ -17,4 +17,10 @@ Read more about our pipelines and repository on the [WARP documentation site](ht
 
 To contribute to WARP, please read the [contribution guidelines](https://broadinstitute.github.io/warp/docs/contribution/README).
 
+### Citing WARP
+
+When citing WARP, please use the following:
+
+Degatano, K.; Awdeh, A.; Dingman, W.; Grant, G.; Khajouei, F.; Kiernan, E.; Konwar, K.; Mathews, K.; Palis, K.; Petrillo, N.; Van der Auwera, G.; Wang, C.; Way, J.; Pipelines, W. WDL Analysis Research Pipelines: Cloud-Optimized Workflows for Biological Data Processing and Reproducible Analysis. Preprints 2024, 2024012131. https://doi.org/10.20944/preprints202401.2131.v1
+
 [![Build Status](https://img.shields.io/github/workflow/status/broadinstitute/warp/Deploy%20WARP%20Website?label=Website&logo=github&style=flat-square)](https://github.com/broadinstitute/warp/actions?query=workflow%3A%22Deploy+WARP+Website%22)
diff --git a/pipelines/broad/annotation_filtration/AnnotationFiltration.changelog.md b/pipelines/broad/annotation_filtration/AnnotationFiltration.changelog.md
@@ -1,3 +1,8 @@
+# 1.2.5
+2023-12-18 (Date of Last Commit)
+
+* Updated to GATK version 4.5.0.0
+
 # 1.2.4
 2022-11-09 (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 = "1.2.4"
+  String pipeline_version = "1.2.5"
 
   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:4.3.0.0"
+    String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.5.0.0"
     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:4.3.0.0",
+  "AnnotationFiltration.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.5.0.0",
   "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:4.3.0.0",
+  "AnnotationFiltration.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.5.0.0",
   "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 @@
+# 1.1.12
+2023-12-18 (Date of Last Commit)
+
+* Updated to GATK version 4.5.0.0
+
 # 1.1.11
 2023-08-01 (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 = "1.1.11"
+  String pipeline_version = "1.1.12"
 
   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 @@
+# 2.6.22
+2023-12-18 (Date of Last Commit)
+
+* Updated to GATK version 4.5.0.0
+
 # 2.6.21
 2023-12-08 (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 = "2.6.21"
+  String pipeline_version = "2.6.22"
 
   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 @@
+# 1.16.4
+2023-12-18 (Date of Last Commit)
+
+* Updated to GATK version 4.5.0.0
+
 # 1.16.3
 2023-01-13 (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 = "1.16.3"
+  String pipeline_version = "1.16.4"
 
   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 @@
+# 1.6.10
+2023-12-18 (Date of Last Commit)
+
+* Updated to GATK version 4.5.0.0
+
 # 1.6.9
 2023-09-08 (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 = "1.6.9"
+  String pipeline_version = "1.6.10"
 
   input {
     File unpadded_intervals_file

diff --git a/...line/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.changelog.md b/...line/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.changelog.md
@@ -1,3 +1,13 @@
+# 1.1.7
+2023-12-18 (Date of Last Commit)
+
+* Updated to GATK version 4.5.0.0.
+
+# 1.1.6
+2023-02-06 (Date of Last Commit)
+
+* Updated VETS filtering pipeline to GATK version 4.5.0.0. Does not affect outputs.
+
 # 1.1.5
 2023-09-08 (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
@@ -1,7 +1,7 @@
 version 1.0
 
 import "../../../../../../tasks/broad/JointGenotypingTasks.wdl" as Tasks
-import "https://raw.githubusercontent.com/broadinstitute/gatk/4.3.0.0/scripts/vcf_site_level_filtering_wdl/JointVcfFiltering.wdl" as Filtering
+import "https://raw.githubusercontent.com/broadinstitute/gatk/4.5.0.0/scripts/vcf_site_level_filtering_wdl/JointVcfFiltering.wdl" as Filtering
 import "../../../../../../tasks/broad/UltimaGenomicsGermlineFilteringThreshold.wdl" as FilteringThreshold
 
 
@@ -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 = "1.1.5"
+  String pipeline_version = "1.1.7"
 
   input {
     File unpadded_intervals_file
@@ -51,10 +51,11 @@ workflow UltimaGenomicsJointGenotyping {
     String flow_order
 
     #inputs for training and applying filter model
-    String snp_annotations
-    String indel_annotations
-    Boolean use_allele_specific_annotations
+    Array[String] snp_annotations
+    Array[String] indel_annotations
     String model_backend
+    String snp_resource_args = "--resource:hapmap,training=true,calibration=true gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz --resource:omni,training=true,calibration=true gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz --resource:1000G,training=true,calibration=false gs://gcp-public-data--broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz"
+    String indel_resource_args = "--resource:mills,training=true,calibration=true gs://gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"
 
     Int? top_level_scatter_count
     Boolean? gather_vcfs
@@ -154,24 +155,42 @@ workflow UltimaGenomicsJointGenotyping {
       disk_size_gb = medium_disk
   }
 
-  call Filtering.JointVcfFiltering as TrainAndApplyFilteringModel {
+  call Filtering.JointVcfFiltering as TrainAndApplyFilteringModelSNPs {
     input:
-      vcf = CalculateAverageAnnotations.output_vcf,
-      vcf_index = CalculateAverageAnnotations.output_vcf_index,
+      input_vcfs = CalculateAverageAnnotations.output_vcf,
+      input_vcf_idxs = CalculateAverageAnnotations.output_vcf_index,
       sites_only_vcf = SitesOnlyGatherVcf.output_vcf,
-      sites_only_vcf_index = SitesOnlyGatherVcf.output_vcf_index,
-      snp_annotations = snp_annotations,
-      indel_annotations = indel_annotations,
+      sites_only_vcf_idx = SitesOnlyGatherVcf.output_vcf_index,
+      annotations = snp_annotations,
+      resource_args = snp_resource_args,
       model_backend = model_backend,
-      use_allele_specific_annotations = use_allele_specific_annotations,
-      basename = callset_name,
-      gatk_docker = "us.gcr.io/broad-gatk/gatk:4.3.0.0"
+      output_prefix = callset_name,
+      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"
+  }
+
+  call Filtering.JointVcfFiltering as TrainAndApplyFilteringModelINDELs {
+    input:
+      input_vcfs = TrainAndApplyFilteringModelSNPs.scored_vcfs,
+      input_vcf_idxs = TrainAndApplyFilteringModelSNPs.scored_vcf_idxs,
+      sites_only_vcf = SitesOnlyGatherVcf.output_vcf,
+      sites_only_vcf_idx = SitesOnlyGatherVcf.output_vcf_index,
+      annotations = indel_annotations,
+      resource_args = indel_resource_args,
+      model_backend = model_backend,
+      output_prefix = callset_name,
+      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"
   }
 
   call FilteringThreshold.ExtractOptimizeSingleSample as FindFilteringThresholdAndFilter {
     input:
-      input_vcf = TrainAndApplyFilteringModel.variant_scored_vcf,
-      input_vcf_index = TrainAndApplyFilteringModel.variant_scored_vcf_index,
+      input_vcf = TrainAndApplyFilteringModelINDELs.scored_vcfs,
+      input_vcf_index = TrainAndApplyFilteringModelINDELs.scored_vcf_idxs,
       base_file_name = callset_name,
       call_sample_name = call_sample_name,
       truth_vcf = truth_vcf,
@@ -188,7 +207,7 @@ workflow UltimaGenomicsJointGenotyping {
       medium_disk = medium_disk
   }
 
-  scatter (idx in range(length(TrainAndApplyFilteringModel.variant_scored_vcf))) {
+  scatter (idx in range(length(TrainAndApplyFilteringModelINDELs.scored_vcfs))) {
     # For large callsets we need to collect metrics from the shards and gather them later.
     if (!is_small_callset) {
       call Tasks.CollectVariantCallingMetrics as CollectMetricsSharded {

diff --git a/...na_seq/germline/joint_genotyping/UltimaGenomics/test_inputs/Plumbing/plumbing.inputs.json b/...na_seq/germline/joint_genotyping/UltimaGenomics/test_inputs/Plumbing/plumbing.inputs.json
@@ -14,17 +14,17 @@
 "UltimaGenomicsJointGenotyping.scatter_cross_check_fingerprints":false,
 "UltimaGenomicsJointGenotyping.unbounded_scatter_count_scale_factor":2.5,
 "UltimaGenomicsJointGenotyping.unpadded_intervals_file":"gs://gcp-public-data--broad-references/hg38/v0/hg38.even.handcurated.20k.intervals",
-"UltimaGenomicsJointGenotyping.snp_annotations": "-A AS_ReadPosRankSum -A AS_FS -A AS_SOR -A AS_QD -A AVERAGE_TREE_SCORE -A AVERAGE_ASSEMBLED_HAPS -A AVERAGE_FILTERED_HAPS",
-"UltimaGenomicsJointGenotyping.indel_annotations": "-A AS_MQRankSum -A AS_ReadPosRankSum -A AS_FS -A AS_SOR -A AS_QD -A AVERAGE_TREE_SCORE",
+"UltimaGenomicsJointGenotyping.snp_annotations": ["AS_ReadPosRankSum", "AS_FS", "AS_SOR", "AS_QD", "AVERAGE_TREE_SCORE", "AVERAGE_ASSEMBLED_HAPS", "AVERAGE_FILTERED_HAPS"],
+"UltimaGenomicsJointGenotyping.indel_annotations": ["AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_SOR", "AS_QD", "AVERAGE_TREE_SCORE"],
 "UltimaGenomicsJointGenotyping.flow_order": "TGCA",
 "UltimaGenomicsJointGenotyping.ref_fasta_sdf": "gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/plumbing/reference_sdf.tar",
 "UltimaGenomicsJointGenotyping.runs_file": "gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/plumbing/runs.conservative.bed",
 "UltimaGenomicsJointGenotyping.annotation_intervals": ["gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/plumbing/LCR-hs38.bed", "gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/plumbing/mappability.0.bed", "gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/plumbing/exome.twist.bed"],
-"UltimaGenomicsJointGenotyping.use_allele_specific_annotations": true,
 "UltimaGenomicsJointGenotyping.truth_vcf":"gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/plumbing/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_PGandRTGphasetransfer.broad-header.vcf.gz",
 "UltimaGenomicsJointGenotyping.truth_vcf_index":"gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/plumbing/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_PGandRTGphasetransfer.broad-header.vcf.gz",
 "UltimaGenomicsJointGenotyping.truth_highconf_intervals": "gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/plumbing/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel_noCENorHET7.bed",
 "UltimaGenomicsJointGenotyping.call_sample_name": "NA12878",
 "UltimaGenomicsJointGenotyping.truth_sample_name": "HG001",
-"UltimaGenomicsJointGenotyping.model_backend": "PYTHON_IFOREST"
+"UltimaGenomicsJointGenotyping.model_backend": "PYTHON_IFOREST",
+"UltimaGenomicsJointGenotyping.TrainAndApplyFilteringModelSNPs.train_runtime_attributes": {"additional_mem_gb":2}
 }
diff --git a/...eq/germline/joint_genotyping/UltimaGenomics/test_inputs/Scientific/scientific.inputs.json b/...eq/germline/joint_genotyping/UltimaGenomics/test_inputs/Scientific/scientific.inputs.json
@@ -14,17 +14,18 @@
 "UltimaGenomicsJointGenotyping.scatter_cross_check_fingerprints":false,
 "UltimaGenomicsJointGenotyping.unbounded_scatter_count_scale_factor":2.5,
 "UltimaGenomicsJointGenotyping.unpadded_intervals_file":"gs://gcp-public-data--broad-references/hg38/v0/hg38.even.handcurated.20k.intervals",
-"UltimaGenomicsJointGenotyping.snp_annotations": "-A AS_ReadPosRankSum -A AS_FS -A AS_SOR -A AS_QD -A AVERAGE_TREE_SCORE -A AVERAGE_ASSEMBLED_HAPS -A AVERAGE_FILTERED_HAPS",
-"UltimaGenomicsJointGenotyping.indel_annotations": "-A AS_MQRankSum -A AS_ReadPosRankSum -A AS_FS -A AS_SOR -A AS_QD -A AVERAGE_TREE_SCORE",
+"UltimaGenomicsJointGenotyping.snp_annotations": ["AS_ReadPosRankSum", "AS_FS", "AS_SOR", "AS_QD", "AVERAGE_TREE_SCORE", "AVERAGE_ASSEMBLED_HAPS", "AVERAGE_FILTERED_HAPS"],
+"UltimaGenomicsJointGenotyping.indel_annotations": ["AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_SOR", "AS_QD", "AVERAGE_TREE_SCORE"],
 "UltimaGenomicsJointGenotyping.flow_order": "TGCA",
 "UltimaGenomicsJointGenotyping.ref_fasta_sdf": "gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/scientific/reference_sdf.tar",
 "UltimaGenomicsJointGenotyping.runs_file": "gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/scientific/runs.conservative.bed",
 "UltimaGenomicsJointGenotyping.annotation_intervals": ["gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/scientific/LCR-hs38.bed", "gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/scientific/mappability.0.bed", "gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/scientific/exome.twist.bed"],
-"UltimaGenomicsJointGenotyping.use_allele_specific_annotations": true,
 "UltimaGenomicsJointGenotyping.truth_vcf":"gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/scientific/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_PGandRTGphasetransfer.broad-header.vcf.gz",
 "UltimaGenomicsJointGenotyping.truth_vcf_index":"gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/scientific/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_PGandRTGphasetransfer.broad-header.vcf.gz",
 "UltimaGenomicsJointGenotyping.truth_highconf_intervals": "gs://broad-gotc-test-storage/UltimaGenomicsJointGenotyping/wgs/scientific/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel_noCENorHET7.bed",
 "UltimaGenomicsJointGenotyping.call_sample_name": "NA12878",
 "UltimaGenomicsJointGenotyping.truth_sample_name": "HG001",
-"UltimaGenomicsJointGenotyping.model_backend": "PYTHON_IFOREST"
+"UltimaGenomicsJointGenotyping.model_backend": "PYTHON_IFOREST",
+"UltimaGenomicsJointGenotyping.TrainAndApplyFilteringModelSNPs.extract_runtime_attributes": {"command_mem_gb":13, "additional_mem_gb":2},
+"UltimaGenomicsJointGenotyping.TrainAndApplyFilteringModelSNPs.train_runtime_attributes": {"command_mem_gb":13, "additional_mem_gb":2}
 }
diff --git a/.../joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md b/.../joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md
@@ -1,3 +1,8 @@
+# 1.4.12
+2023-12-18 (Date of Last Commit)
+
+* Updated to GATK version 4.5.0.0
+
 # 1.4.11
 2023-09-08 (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 = "1.4.11"
+  String pipeline_version = "1.4.12"
 
   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 @@
+# 1.4.11
+2023-12-18 (Date of Last Commit)
+
+* Updated to GATK version 4.5.0.0
+
 # 1.4.10
 2023-09-08 (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 = "1.4.10"
+  String pipeline_version = "1.4.11"
 
   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
@@ -1,10 +1,14 @@
+# 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.
+
 # 2.1.10
 2023-12-14 (Date of Last Commit)
 
 * Updated GATK for Reblock task to version 4.5.0.0
 * Added options to Reblock task to remove annotations and move filters to genotype level
 
-
 # 2.1.9
 2023-12-08 (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
@@ -5,7 +5,7 @@ import "../../../../../../tasks/broad/Qc.wdl" as QC
 
 workflow ReblockGVCF {
 
-  String pipeline_version = "2.1.10"
+  String pipeline_version = "2.1.11"
 
 
   input {
@@ -50,7 +50,7 @@ workflow ReblockGVCF {
         calling_interval_list_index = gvcf_index,
         is_gvcf = true,
         extra_args = "--no-overlaps",
-        gatk_docker = "us.gcr.io/broad-gatk/gatk:4.3.0.0"
+        gatk_docker = "us.gcr.io/broad-gatk/gatk:4.5.0.0"
     }
 
   output {

diff --git a/...oad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.changelog.md b/...oad/dna_seq/germline/single_sample/exome/ExomeGermlineSingleSample.changelog.md
@@ -1,10 +1,14 @@
+# 3.1.18
+2023-12-18 (Date of Last Commit)
+
+* Updated to GATK version 4.5.0.0.
+
 # 3.1.17
 2023-12-14 (Date of Last Commit)
 
 * Updated GATK for Reblock task to version 4.5.0.0
 * Added options to Reblock task to remove annotations and move filters to genotype level
 
-
 # 3.1.16
 2023-12-08 (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
@@ -44,7 +44,7 @@ import "../../../../../../structs/dna_seq/DNASeqStructs.wdl"
 # WORKFLOW DEFINITION
 workflow ExomeGermlineSingleSample {
 
-  String pipeline_version = "3.1.17"
+  String pipeline_version = "3.1.18"
 
 
   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 @@
+# 1.0.15
+2023-12-18 (Date of Last Commit)
+
+* Updated to GATK version 4.5.0.0.
+
 # 1.0.14
 2023-12-14 (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 = "1.0.14"
+  String pipeline_version = "1.0.15"
 
 
   References references = alignment_references.references