Merge branch 'develop' into np_update_gatk_4.6.1.0_revert_BQSR

broadinstitute · Nov 1, 2024 · 2912c0e · 2912c0e
2 parents 038a344 + 70d3e1d
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diff --git a/pipeline_versions.txt b/pipeline_versions.txt
@@ -1,40 +1,40 @@
 Pipeline Name	Version	Date of Last Commit
-CheckFingerprint	 1.0.21	2024-09-06 
+CheckFingerprint	 1.0.22	2024-10-28 
 RNAWithUMIsPipeline	 1.0.17	2024-09-06 
 AnnotationFiltration	 1.2.6	2024-09-06 
-UltimaGenomicsWholeGenomeGermline	 1.1.0	2024-09-06 
-WholeGenomeGermlineSingleSample	 3.3.1	2024-09-17 
-ExomeGermlineSingleSample	 3.2.1	2024-09-17 
+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	 2.3.0	2024-09-06 
+ReblockGVCF	 2.3.1	2024-10-28 
 JointGenotyping	 1.7.1	2024-09-10 
 UltimaGenomicsJointGenotyping	 1.2.1	2024-09-10 
-VariantCalling	 2.2.2	2024-09-06 
-UltimaGenomicsWholeGenomeCramOnly	 1.0.21	2024-09-06 
+VariantCalling	 2.2.3	2024-10-28 
+UltimaGenomicsWholeGenomeCramOnly	 1.0.22	2024-10-28 
 GDCWholeGenomeSomaticSingleSample	 1.3.3	2024-09-06 
-BroadInternalRNAWithUMIs	 1.0.34	2024-09-06 
-BroadInternalUltimaGenomics	 1.1.0	2024-09-06 
-BroadInternalArrays	 1.1.12	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	 2.6.28	2024-09-06 
+Arrays	 2.6.29	2024-10-28 
 ValidateChip	 1.16.6	2024-09-06 
 MultiSampleArrays	 1.6.2	2024-08-02 
 Imputation	 1.1.14	2024-09-06 
-IlluminaGenotypingArray	 1.12.22	2024-09-06 
-ExternalWholeGenomeReprocessing	 2.3.1	2024-09-17 
-ExternalExomeReprocessing	 3.3.1	2024-09-17 
+IlluminaGenotypingArray	 1.12.23	2024-10-28 
+ExternalWholeGenomeReprocessing	 2.3.2	2024-10-28 
+ExternalExomeReprocessing	 3.3.2	2024-10-28 
 CramToUnmappedBams	 1.1.3	2024-08-02 
-WholeGenomeReprocessing	 3.3.1	2024-09-17 
-ExomeReprocessing	 3.3.1	2024-09-17 
+WholeGenomeReprocessing	 3.3.2	2024-10-28 
+ExomeReprocessing	 3.3.2	2024-10-28 
 BuildIndices	 3.0.0	2023-12-06 
 scATAC	 1.3.2	2023-08-03 
 snm3C	 4.0.4	2024-08-06 
-Multiome	 5.7.1	2024-10-18 
-PairedTag	 1.7.1	2024-10-18 
+Multiome	 5.8.0	2024-10-23 
+PairedTag	 1.8.0	2024-10-23 
 MultiSampleSmartSeq2	 2.2.22	2024-09-11 
-MultiSampleSmartSeq2SingleNucleus	 2.0.1	2024-09-24 
-Optimus	 7.7.0	2024-09-24 
-atac	 2.3.2	2024-10-18 
+MultiSampleSmartSeq2SingleNucleus	 2.0.2	2024-10-23 
+Optimus	 7.8.0	2024-10-23 
+atac	 2.4.0	2024-10-23 
 SmartSeq2SingleSample	 5.1.21	2024-09-11 
-SlideSeq	 3.4.2	2024-09-24 
+SlideSeq	 3.4.3	2024-10-24 
diff --git a/pipelines/broad/arrays/single_sample/Arrays.changelog.md b/pipelines/broad/arrays/single_sample/Arrays.changelog.md
@@ -1,3 +1,8 @@
+# 2.6.29
+2024-10-28 (Date of Last Commit)
+
+* Updated the docker in the ValidateVCF task; this does not affect this pipeline
+
 # 2.6.28
 2024-09-06 (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 = "2.6.28"
+  String pipeline_version = "2.6.29"
 
   input {
     String chip_well_barcode

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 @@
+# 2.3.1
+2024-10-28 (Date of Last Commit)
+
+* Updated GATK for Validate Variants, which reduces the memory requirements for the task when an interval list is not provided
+
 # 2.3.0
 2024-09-06 (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 = "2.3.0"
+  String pipeline_version = "2.3.1"
 
 
   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 @@
+# 3.2.2
+2024-10-28 (Date of Last Commit)
+
+* Updated the docker in the ValidateVCF task; this does not affect this pipeline
+
 # 3.2.1
 2024-09-17 (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 = "3.2.1"
+  String pipeline_version = "3.2.2"
 
 
   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 @@
+# 1.1.1
+2024-10-28 (Date of Last Commit)
+
+* Updated the docker in the ValidateVCF task; this does not affect this pipeline
+
 # 1.1.0
 2024-09-06 (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 = "1.1.0"
+  String pipeline_version = "1.1.1"
 
 
   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 @@
+# 3.3.2
+2024-10-28 (Date of Last Commit)
+
+* Updated the docker in the ValidateVCF task; this does not affect this pipeline
+
 # 3.3.1
 2024-09-17 (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 = "3.3.1"
+  String pipeline_version = "3.3.2"
 
 
   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 @@
+# 2.2.3
+2024-10-28 (Date of Last Commit)
+
+* Updated the docker in the ValidateVCF task; this does not affect this pipeline
+
 # 2.2.2
 2024-09-06 (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 = "2.2.2"
+  String pipeline_version = "2.2.3"
 
 
   input {

diff --git a/..._seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.changelog.md b/..._seq/somatic/single_sample/ugwgs/UltimaGenomicsWholeGenomeCramOnly.changelog.md
@@ -1,3 +1,8 @@
+# 1.0.22
+2024-10-28 (Date of Last Commit)
+
+* Updated the docker in the ValidateVCF task; this does not affect this pipeline
+
 # 1.0.21
 2024-09-06 (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 = "1.0.21"
+  String pipeline_version = "1.0.22"
 
   References references = alignment_references.references
 

diff --git a/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.changelog.md b/pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.changelog.md
@@ -1,3 +1,8 @@
+# 1.12.23
+2024-10-28 (Date of Last Commit)
+
+* Updated the docker in the ValidateVCF task; this does not affect this pipeline
+
 # 1.12.22
 2024-09-06 (Date of Last Commit)
 

diff --git 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 = "1.12.22"
+  String pipeline_version = "1.12.23"
 
   input {
     String sample_alias

diff --git a/pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.changelog.md b/pipelines/broad/internal/arrays/single_sample/BroadInternalArrays.changelog.md
@@ -1,3 +1,8 @@
+# 1.1.13
+2024-10-28 (Date of Last Commit)
+
+* Updated the docker in the ValidateVCF task; this does not affect this pipeline
+
 # 1.1.12
 2024-09-06 (Date of Last Commit)
 

diff --git 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 = "1.1.12"
+    String pipeline_version = "1.1.13"
 
     input {
         # inputs to wrapper task

diff --git a/.../germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.changelog.md b/.../germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.changelog.md
@@ -1,3 +1,8 @@
+# 1.1.1
+2024-10-28 (Date of Last Commit)
+
+* Updated the docker in the ValidateVCF task; this does not affect this pipeline
+
 # 1.1.0
 2024-09-06 (Date of Last Commit)
 

diff --git a/...ad/internal/dna_seq/germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.wdl b/...ad/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 = "1.1.0"
+  String pipeline_version = "1.1.1"
 
   input {
 

diff --git a/pipelines/broad/internal/rna_seq/BroadInternalRNAWithUMIs.changelog.md b/pipelines/broad/internal/rna_seq/BroadInternalRNAWithUMIs.changelog.md
@@ -1,3 +1,8 @@
+# 1.0.35
+2024-09-06 (Date of Last Commit)
+
+* Updated the docker in the ValidateVCF task; this does not affect this pipeline
+
 # 1.0.34
 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
@@ -7,7 +7,7 @@ import "../../../../tasks/broad/Utilities.wdl" as utils
 
 workflow BroadInternalRNAWithUMIs {
 
-  String pipeline_version = "1.0.34"
+  String pipeline_version = "1.0.35"
 
   input {
     # input needs to be either "hg19" or "hg38"

diff --git a/pipelines/broad/qc/CheckFingerprint.changelog.md b/pipelines/broad/qc/CheckFingerprint.changelog.md
@@ -1,3 +1,8 @@
+# 1.0.22
+2024-10-28 (Date of Last Commit)
+
+* Updated the docker in the ValidateVCF task; this does not affect this pipeline
+
 # 1.0.21
 2024-09-06 (Date of Last Commit)
 

diff --git a/pipelines/broad/qc/CheckFingerprint.wdl b/pipelines/broad/qc/CheckFingerprint.wdl
@@ -24,7 +24,7 @@ import "../../../tasks/broad/Qc.wdl" as Qc
 
 workflow CheckFingerprint {
 
-  String pipeline_version = "1.0.21"
+  String pipeline_version = "1.0.22"
 
   input {
     File? input_vcf

diff --git a/pipelines/broad/reprocessing/exome/ExomeReprocessing.changelog.md b/pipelines/broad/reprocessing/exome/ExomeReprocessing.changelog.md
@@ -1,3 +1,8 @@
+# 3.3.2
+2024-10-28 (Date of Last Commit)
+
+* Updated the docker in the ValidateVCF task; this does not affect this pipeline
+
 # 3.3.1
 2024-09-17 (Date of Last Commit)
 

diff --git 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 = "3.3.1"
+  String pipeline_version = "3.3.2"
 
   input {
     File? input_cram

diff --git a/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.changelog.md b/pipelines/broad/reprocessing/external/exome/ExternalExomeReprocessing.changelog.md
@@ -1,3 +1,8 @@
+# 3.3.2
+2024-10-28 (Date of Last Commit)
+
+* Updated the docker in the ValidateVCF task; this does not affect this pipeline
+
 # 3.3.1
 2024-09-17 (Date of Last Commit)
 

diff --git 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 = "3.3.1"
+  String pipeline_version = "3.3.2"
 
 
   input {

diff --git a/...es/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.changelog.md b/...es/broad/reprocessing/external/wgs/ExternalWholeGenomeReprocessing.changelog.md
@@ -1,3 +1,8 @@
+# 2.3.2
+2024-10-28 (Date of Last Commit)
+
+* Updated the docker in the ValidateVCF task; this does not affect this pipeline
+
 # 2.3.1
 2024-09-17 (Date of Last Commit)
 

diff --git 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 = "2.3.1"
+  String pipeline_version = "2.3.2"
 
   input {
     File? input_cram

diff --git a/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.changelog.md b/pipelines/broad/reprocessing/wgs/WholeGenomeReprocessing.changelog.md
@@ -1,3 +1,8 @@
+# 3.3.2
+2024-10-28 (Date of Last Commit)
+
+* Updated the docker in the ValidateVCF task; this does not affect this pipeline
+
 # 3.3.1
 2024-09-17 (Date of Last Commit)
 

diff --git 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 = "3.3.1"
+  String pipeline_version = "3.3.2"
 
   input {
     File? input_cram

diff --git a/pipelines/skylab/atac/atac.changelog.md b/pipelines/skylab/atac/atac.changelog.md
@@ -1,3 +1,12 @@
+# 2.4.0
+2024-10-23 (Date of Last Commit)
+
+* Added a new input parameter for atac_expected_cells, which describes the numnber of cells used for the library preparation
+* Updated the ATAC library CSV to be consistent in file naming convention and to have similar case for metric names to the Optimus workflow library CSV
+* Added a new metric to the ATAC library CSV to calculate percent_target, which is the number of estimated cells by SnapATAC2 divided by expected_cells input
+* Updated the ATAC workflow so that the output fragment file is bgzipped by default
+
+
 # 2.3.2
 2024-10-18 (Date of Last Commit)
-Original file line number
+Diff line change
@@ Expand Up / @@ -6,7 +6,7 @@ import "../../../../../../tasks/broad/Utilities.wdl" as utils @@
     workflow ReblockGVCF {
-      String pipeline_version = "2.3.0"
+      String pipeline_version = "2.3.1"
       input {
@@ Expand Down @@