broadinstitute · nikellepetrillo · Dec 13, 2023 · Dec 7, 2023 · Dec 8, 2023 · Dec 8, 2023
diff --git a/pipelines/broad/arrays/single_sample/Arrays.changelog.md b/pipelines/broad/arrays/single_sample/Arrays.changelog.md
@@ -1,3 +1,8 @@
+# 2.6.21
+2023-12-08 (Date of Last Commit)
+
+* ValidateVcfs now has optional memory parameter; this does not affect this pipeline
+
 # 2.6.20
 2023-11-29 (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 = "2.6.20"
+  String pipeline_version = "2.6.21"
 
   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 @@
+# 2.1.9
+2023-12-08 (Date of Last Commit)
+
+* ValidateVcfs now has optional memory parameter
+
 # 2.1.8
 2023-11-29 (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 = "2.1.8"
+  String pipeline_version = "2.1.9"
 
 
   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 @@
+# 3.1.16
+2023-12-08 (Date of Last Commit)
+
+* ValidateVcfs now has optional memory parameter; this does not affect this pipeline
+
 # 3.1.15
 2023-11-29 (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 = "3.1.15"
+  String pipeline_version = "3.1.16"
 
 
   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 @@
+# 1.0.13
+2023-12-08 (Date of Last Commit)
+
+* ValidateVcfs now has optional memory parameter; this does not affect this pipeline
+
 # 1.0.12
 2023-11-29 (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 = "1.0.12"
+  String pipeline_version = "1.0.13"
 
 
   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 @@
+# 3.1.17
+2023-12-08 (Date of Last Commit)
+
+* ValidateVcfs now has optional memory parameter; this does not affect this pipeline
+
 # 3.1.16
 2023-11-29 (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 = "3.1.16"
+  String pipeline_version = "3.1.17"
 
 
   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 @@
+# 2.1.15
+2023-12-08 (Date of Last Commit)
+
+* ValidateVcfs now has optional memory parameter; this does not affect this pipeline
+
 # 2.1.14
 2023-11-29 (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 = "2.1.14"
+  String pipeline_version = "2.1.15"
 
 
   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 @@
+# 1.0.13
+2023-12-08 (Date of Last Commit)
+
+* ValidateVcfs now has optional memory parameter; this does not affect this pipeline
+
 # 1.0.12
 2023-11-29 (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 = "1.0.12"
+  String pipeline_version = "1.0.13"
 
   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 @@
+# 1.12.15
+2023-12-08 (Date of Last Commit)
+
+* ValidateVcfs now has optional memory parameter; this does not affect this pipeline
+
 # 1.12.14
 2023-11-29 (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 = "1.12.14"
+  String pipeline_version = "1.12.15"
 
   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 @@
+# 1.1.5
+2023-12-08 (Date of Last Commit)
+
+* ValidateVcfs now has optional memory parameter; this does not affect this pipeline
+
 # 1.1.4
 2023-11-29 (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 = "1.1.4"
+    String pipeline_version = "1.1.5"
 
     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 @@
+# 1.0.14
+2023-12-08 (Date of Last Commit)
+
+* ValidateVcfs now has optional memory parameter; this does not affect this pipeline
+
 # 1.0.13
 2023-11-29 (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 = "1.0.13"
+  String pipeline_version = "1.0.14"
 
   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 @@
+# 1.0.27
+2023-12-08 (Date of Last Commit)
+
+* ValidateVcfs now has optional memory parameter; this does not affect this pipeline
+
 # 1.0.26
 2023-11-29 (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 = "1.0.26"
+  String pipeline_version = "1.0.27"
 
   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 @@
+# 1.0.14
+2023-12-08 (Date of Last Commit)
+
+* ValidateVcfs now has optional memory parameter; this does not affect this pipeline
+
 # 1.0.13
 2023-11-29 (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 = "1.0.13"
+  String pipeline_version = "1.0.14"
 
   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 @@
+# 3.1.16
+2023-12-08 (Date of Last Commit)
+
+* ValidateVcfs now has optional memory parameter; this does not affect this pipeline
+
 # 3.1.15
 2023-11-29 (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 = "3.1.15"
+  String pipeline_version = "3.1.16"
 
   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 @@
+# 3.1.18
+2023-12-08 (Date of Last Commit)
+
+* ValidateVcfs now has optional memory parameter; this does not affect this pipeline
+
 # 3.1.17
 2023-11-29 (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 = "3.1.17"
+  String pipeline_version = "3.1.18"
 
 
   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 @@
+# 2.1.18
+2023-12-08 (Date of Last Commit)
+
+* ValidateVcfs now has optional memory parameter; this does not affect this pipeline
+
 # 2.1.17
 2023-11-29 (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 = "2.1.17"
+  String pipeline_version = "2.1.18"
 
   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 @@
+# 3.1.17
+2023-12-08 (Date of Last Commit)
+
+* ValidateVcfs now has optional memory parameter; this does not affect this pipeline
+
 # 3.1.16
 2023-11-29 (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 = "3.1.16"
+  String pipeline_version = "3.1.17"
 
   input {
     File? input_cram

diff --git a/pipelines/skylab/multiome/Multiome.changelog.md b/pipelines/skylab/multiome/Multiome.changelog.md
@@ -1,3 +1,8 @@
+# 3.0.1
+2023-12-08 (Date of Last Commit)
+
+* ValidateVcfs now has optional memory parameter; this does not affect this pipeline
+
 # 3.0.0
 2023-11-22 (Date of Last Commit)
 

diff --git a/pipelines/skylab/multiome/Multiome.wdl b/pipelines/skylab/multiome/Multiome.wdl
@@ -6,7 +6,7 @@ import "../../../tasks/skylab/H5adUtils.wdl" as H5adUtils
 import "https://raw.githubusercontent.com/broadinstitute/CellBender/v0.3.0/wdl/cellbender_remove_background.wdl" as CellBender
 
 workflow Multiome {
-    String pipeline_version = "3.0.0"
+    String pipeline_version = "3.0.1"
 
     input {
         String input_id

diff --git a/tasks/broad/Qc.wdl b/tasks/broad/Qc.wdl
@@ -622,12 +622,14 @@ task ValidateVCF {
     Boolean is_gvcf = true
     String? extra_args
     String gatk_docker = "us.gcr.io/broad-gatk/gatk:4.3.0.0"
+    Int machine_mem_mb = 7000
   }
 
   Boolean calling_intervals_is_vcf = defined(calling_interval_list_index)
   String calling_interval_list_basename = basename(calling_interval_list)
   String calling_interval_list_index_basename = if calling_intervals_is_vcf then basename(select_first([calling_interval_list_index])) else ""
 
+  Int command_mem_mb = machine_mem_mb - 1000
   Float ref_size = size(ref_fasta, "GiB") + size(ref_fasta_index, "GiB") + size(ref_dict, "GiB")
   Int disk_size = ceil(size(input_vcf, "GiB") + size(dbsnp_vcf, "GiB") + ref_size) + 20
 
@@ -641,7 +643,7 @@ task ValidateVCF {
     fi
 
     # Note that WGS needs a lot of memory to do the -L *.vcf if an interval file is not supplied
-    gatk --java-options "-Xms6000m -Xmx6500m" \
+    gatk --java-options "-Xms~{command_mem_mb}m -Xmx~{command_mem_mb}m" \
       ValidateVariants \
       -V ~{input_vcf} \
       -R ~{ref_fasta} \
@@ -654,7 +656,7 @@ task ValidateVCF {
   runtime {
     docker: gatk_docker
     preemptible: preemptible_tries
-    memory: "7000 MiB"
+    memory: machine_mem_mb + " MiB"
     bootDiskSizeGb: 15
     disks: "local-disk " + disk_size + " HDD"
   }

diff --git a/website/docs/Pipelines/Exome_Germline_Single_Sample_Pipeline/README.md b/website/docs/Pipelines/Exome_Germline_Single_Sample_Pipeline/README.md
@@ -7,7 +7,7 @@ slug: /Pipelines/Exome_Germline_Single_Sample_Pipeline/README
 
 | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
 | :----: | :---: | :----: | :--------------: |
-| [ExomeGermlineSingleSample_v3.1.15](https://github.com/broadinstitute/warp/releases?q=ExomeGermlineSingleSample_v3.0.0&expanded=true) | December, 2023 | [Elizabeth Kiernan](mailto:[email protected]) | Please file GitHub issues in WARP or contact [the WARP team](mailto:[email protected]) |
+| [ExomeGermlineSingleSample_v3.1.16](https://github.com/broadinstitute/warp/releases?q=ExomeGermlineSingleSample_v3.0.0&expanded=true) | December, 2023 | [Elizabeth Kiernan](mailto:[email protected]) | Please file GitHub issues in WARP or contact [the WARP team](mailto:[email protected]) |
 
 
 The Exome Germline Single Sample pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human exome sequencing data.

diff --git a/website/docs/Pipelines/Multiome_Pipeline/README.md b/website/docs/Pipelines/Multiome_Pipeline/README.md
@@ -7,7 +7,7 @@ slug: /Pipelines/Multiome_Pipeline/README
 
 | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
 | :----: | :---: | :----: | :--------------: |
-| [Multiome v3.0.0](https://github.com/broadinstitute/warp/releases) | December, 2023 | Kaylee Mathews | Please file GitHub issues in warp or contact the [WARP Pipeline Development team](mailto:[email protected]) |
+| [Multiome v3.0.1](https://github.com/broadinstitute/warp/releases) | December, 2023 | Kaylee Mathews | Please file GitHub issues in warp or contact the [WARP Pipeline Development team](mailto:[email protected]) |
 
 ![Multiome_diagram](./multiome_diagram.png)
 

diff --git a/website/docs/Pipelines/Ultima_Genomics_Whole_Genome_Germline_Pipeline/README.md b/website/docs/Pipelines/Ultima_Genomics_Whole_Genome_Germline_Pipeline/README.md
@@ -7,7 +7,7 @@ slug: /Pipelines/Ultima_Genomics_Whole_Genome_Germline_Pipeline/README
 
 | Pipeline Version | Date Updated | Documentation Authors | Questions or Feedback |
 | :----: | :---: | :----: | :--------------: |
-| [UltimaGenomicsWholeGenomeGermline_v1.0.0](https://github.com/broadinstitute/warp/releases) | June, 2022 | [Elizabeth Kiernan](mailto:[email protected]) & [Kaylee Mathews](mailto:[email protected])| Please file GitHub issues in warp or contact [the wARP team](mailto:[email protected]) |
+| [UltimaGenomicsWholeGenomeGermline_v1.0.13](https://github.com/broadinstitute/warp/releases) | December, 2023 | [Elizabeth Kiernan](mailto:[email protected]) & [Kaylee Mathews](mailto:[email protected])| Please file GitHub issues in warp or contact [the wARP team](mailto:[email protected]) |
 
 ![UG_diagram](ug_diagram.png)
 
@@ -19,7 +19,7 @@ The [Ultima Genomics Whole Genome Germline (UG_WGS) workflow](https://github.com
 
 Ultima Genomics sequencing is a novel technology that produces single-read, flow-based data ([Almogy et al., 2022](https://www.biorxiv.org/content/10.1101/2022.05.29.493900v1)). The sequencing platform works by flowing one nucleotide at a time in order, iteratively. This is in contrast to traditional technologies that do all four nucleotides at once. This iterative approach ensures that only one dNTP is responsible for the signal and it does not require the blocking of dNTPs.  
 
-### What does the workflow do? 
+### What does the workflow do?
 
 The workflow requires either an aligned CRAM output of the sequencing platform or an unmapped BAM as input. Overall, it aligns reads to a reference genome, marks duplicate reads, calls variants, post-processes variants in the output VCF in preparation for joint calling, and calculates quality control metrics. The workflow outputs a (re)aligned CRAM, an annotated GVCF with index, and quality metrics. 
 
@@ -201,7 +201,7 @@ The workflow implements initial variant calling with a version of HaplotypeCalle
 | [Utilities.ScatterIntervalList](https://github.com/broadinstitute/warp/blob/develop/tasks/broad/Utilities.wdl) | IntervalListTools | Picard | Splits the calling interval list into sub-intervals in order to perform variant calling on the sub-intervals. |
 | [Tasks.HaplotypeCaller](https://github.com/broadinstitute/warp/blob/develop/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl) | HaplotypeCaller | GATK | Performs initial variant calling on the aligned BAM file and outputs sub-interval GVCFs and a bamout file. |
 
-### 6. Merge VCFs and BAMs and convert GVCF to VCF 
+### 6. Merge VCFs and BAMs and convert GVCF to VCF
 The workflow performs multiple post-processing steps to prepare the VCF for downstream joint calling. The HaplotypeCaller GVCF outputs are merged into a single GVCF and then converted to VCF in preparation for this post-processing.
 
 | Task name and WDL link | Tool | Software | Description | 

diff --git a/website/docs/Pipelines/Whole_Genome_Germline_Single_Sample_Pipeline/README.md b/website/docs/Pipelines/Whole_Genome_Germline_Single_Sample_Pipeline/README.md
@@ -7,7 +7,7 @@ slug: /Pipelines/Whole_Genome_Germline_Single_Sample_Pipeline/README
 
 | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
 | :----: | :---: | :----: | :--------------: |
-| WholeGenomeGermlineSingleSample_v3.1.14 (see [releases page](https://github.com/broadinstitute/warp/releases)) | August, 2022 | [Elizabeth Kiernan](mailto:[email protected]) | Please file GitHub issues in WARP or contact [the WARP team](mailto:[email protected]) |
+| WholeGenomeGermlineSingleSample_v3.1.17 (see [releases page](https://github.com/broadinstitute/warp/releases)) | December, 2023 | [Elizabeth Kiernan](mailto:[email protected]) | Please file GitHub issues in WARP or contact [the WARP team](mailto:[email protected]) |
 
 ## Introduction to the Whole Genome Germline Single Sample Pipeline
 The Whole Genome Germline Single Sample (WGS) pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human whole-genome sequencing data. It includes the DRAGEN-GATK mode, which makes the pipeline functionally equivalent to DRAGEN’s analysis pipeline (read more in this [DRAGEN-GATK blog](https://gatk.broadinstitute.org/hc/en-us/articles/360039984151)).
-Original file line number
+Diff line change
@@ Expand Up / @@ -5,7 +5,7 @@ import "../../../../../../tasks/broad/Qc.wdl" as QC @@
     workflow ReblockGVCF {
-      String pipeline_version = "2.1.8"
+      String pipeline_version = "2.1.9"
       input {
@@ Expand Down @@