broadinstitute · meganshand · Sep 19, 2023 · Sep 18, 2023 · Sep 18, 2023
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 @@
+# 2.1.6
+2023-09-18 (Date of Last Commit)
+
+* ReblockGVCFs can now take in GVCFs that are not in the same location as their index file
+
 # 2.1.5
 2023-03-20 (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 = "2.1.5"
+  String pipeline_version = "2.1.6"
 
 
   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 @@
+# 3.1.12
+2023-09-18 (Date of Last Commit)
+
+* ReblockGVCFs can now take in GVCFs that are not in the same location as their index file, this update has no effect on this pipeline.
+
 # 3.1.11
 2023-08-23 (Date of Last Commit)
 * Updated VerifyBamID docker image in BamProcessing.wdl to fix security vulnerabilities, this update has no effect on this pipeline.  

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 = "3.1.11"
+  String pipeline_version = "3.1.12"
 
 
   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 @@
+# 1.0.10
+2023-09-18 (Date of Last Commit)
+
+* ReblockGVCFs can now take in GVCFs that are not in the same location as their index file, this update has no effect on this pipeline.
+
 # 1.0.9
 2023-08-16 (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 = "1.0.9"
+  String pipeline_version = "1.0.10"
 
 
   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 @@
+# 3.1.13
+2023-09-18 (Date of Last Commit)
+
+* ReblockGVCFs can now take in GVCFs that are not in the same location as their index file, this update has no effect on this pipeline.
+
 # 3.1.12
 2023-08-23 (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 = "3.1.12"
+  String pipeline_version = "3.1.13"
 
 
   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 @@
+# 2.1.12
+2023-09-18 (Date of Last Commit)
+
+* ReblockGVCFs can now take in GVCFs that are not in the same location as their index file, this update has no effect on this pipeline.
+
 # 2.1.11
 2023-08-23 (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 = "2.1.11"
+  String pipeline_version = "2.1.12"
 
 
   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 @@
+# 1.0.10
+2023-09-18 (Date of Last Commit)
+
+* ReblockGVCFs can now take in GVCFs that are not in the same location as their index file, this update has no effect on this pipeline.
+
 # 1.0.9
 2023-08-16 (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 = "1.0.9"
+  String pipeline_version = "1.0.10"
 
   References references = alignment_references.references
 

diff --git a/.../germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.changelog.md b/.../germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.changelog.md
@@ -1,3 +1,8 @@
+# 1.0.11
+2023-09-18 (Date of Last Commit)
+
+* ReblockGVCFs can now take in GVCFs that are not in the same location as their index file, this update has no effect on this pipeline.
+
 # 1.0.10
 2023-08-16 (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 = "1.0.10"
+  String pipeline_version = "1.0.11"
 
   input {
 

diff --git a/pipelines/broad/reprocessing/exome/ExomeReprocessing.changelog.md b/pipelines/broad/reprocessing/exome/ExomeReprocessing.changelog.md
@@ -1,3 +1,8 @@
+# 3.1.12
+2023-09-18 (Date of Last Commit)
+
+* ReblockGVCFs can now take in GVCFs that are not in the same location as their index file, this update has no effect on this pipeline.
+
 # 3.1.11
 2023-08-23 (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 = "3.1.11"
+  String pipeline_version = "3.1.12"
 
   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 @@
+# 3.1.14
+2023-09-18 (Date of Last Commit)
+
+* ReblockGVCFs can now take in GVCFs that are not in the same location as their index file, this update has no effect on this pipeline.
+
 # 3.1.13
 2023-08-23 (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 = "3.1.13"
+  String pipeline_version = "3.1.14"
 
 
   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 @@
+# 2.1.14
+2023-09-18 (Date of Last Commit)
+
+* ReblockGVCFs can now take in GVCFs that are not in the same location as their index file, this update has no effect on this pipeline.
+
 # 2.1.13
 2023-08-23 (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 = "2.1.13"
+  String pipeline_version = "2.1.14"
 
   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 @@
+# 3.1.13
+2023-09-18 (Date of Last Commit)
+
+* ReblockGVCFs can now take in GVCFs that are not in the same location as their index file, this update has no effect on this pipeline.
+
 # 3.1.12
 2023-08-23 (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 = "3.1.12"
+  String pipeline_version = "3.1.13"
 
   input {
     File? input_cram

diff --git a/tasks/broad/GermlineVariantDiscovery.wdl b/tasks/broad/GermlineVariantDiscovery.wdl
@@ -210,10 +210,16 @@ task Reblock {
   }
 
   Int disk_size = ceil((size(gvcf, "GiB")) * 4) + additional_disk
+  String gvcf_basename = basename(gvcf)
+  String gvcf_index_basename = basename(gvcf_index)
 
   command {
     set -e 
 
+    # We can't always assume the index was located with the gvcf, so make a link so that the paths look the same
+    ln -s ~{gvcf} ~{gvcf_basename}
+    ln -s ~{gvcf_index} ~{gvcf_index_basename}
+
     gatk --java-options "-Xms3000m -Xmx3000m" \
       ReblockGVCF \
       -R ~{ref_fasta} \
-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 = "2.1.5"
+      String pipeline_version = "2.1.6"
       input {
@@ Expand Down @@