Update output names for ReblockGVCF (#1443)

* Update output names for ReblockGVCF --------- Co-authored-by: GitHub Action <[email protected]>
broadinstitute · Jan 8, 2025 · 6e9963c · 6e9963c
1 parent 642e3f2
commit 6e9963c
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Showing 8 changed files with 29 additions and 14 deletions.
diff --git a/pipeline_versions.txt b/pipeline_versions.txt
@@ -2,19 +2,19 @@ Pipeline Name	Version	Date of Last Commit
 CheckFingerprint	 1.0.22	2024-10-28 
 RNAWithUMIsPipeline	 1.0.18	2024-11-04 
 AnnotationFiltration	 1.2.7	2024-11-04 
-UltimaGenomicsWholeGenomeGermline	 1.1.2	2024-11-04 
+UltimaGenomicsWholeGenomeGermline	 1.1.3	2024-12-05 
 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 
+ReblockGVCF	 2.4.0	2024-12-05 
 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 
+BroadInternalUltimaGenomics	 1.1.3	2024-12-05 
 BroadInternalArrays	 1.1.14	2024-11-04 
 BroadInternalImputation	 1.1.14	2024-11-04 
 Arrays	 2.6.30	2024-11-04 

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 @@
+# 2.4.0
+2024-12-05 (Date of Last Commit)
+
+* Updated output names for ReblockGVCF workflow from output_vcf and output_vcf_index to reblocked_gvcf and reblocked_gvcf_index respectively
+
 # 2.3.2
 2024-11-04 (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 = "2.3.2"
+  String pipeline_version = "2.4.0"
 
 
   input {
@@ -70,8 +70,8 @@ workflow ReblockGVCF {
     }
 
   output {
-    File output_vcf = Reblock.output_vcf
-    File output_vcf_index = Reblock.output_vcf_index
+    File reblocked_gvcf = Reblock.output_vcf
+    File reblocked_gvcf_index = Reblock.output_vcf_index
   }
   meta {
     allowNestedInputs: true

diff --git a/...seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.changelog.md b/...seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.changelog.md
@@ -1,3 +1,8 @@
+# 1.1.3
+2024-12-05 (Date of Last Commit)
+
+* Updated the name of the output for ReblockGVCFs; this does not affect this pipeline
+
 # 1.1.2
 2024-11-04 (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 = "1.1.2"
+  String pipeline_version = "1.1.3"
 
 
   References references = alignment_references.references
@@ -202,8 +202,8 @@ workflow UltimaGenomicsWholeGenomeGermline {
 
   # Outputs that will be retained when execution is complete
   output {
-    File output_gvcf = ReblockGVCF.output_vcf
-    File output_gvcf_index = ReblockGVCF.output_vcf_index
+    File output_gvcf = ReblockGVCF.reblocked_gvcf
+    File output_gvcf_index = ReblockGVCF.reblocked_gvcf_index
     File output_vcf = ConvertGVCFtoVCF.output_vcf
     File output_vcf_index = ConvertGVCFtoVCF.output_vcf_index
 

diff --git a/.../germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.changelog.md b/.../germline/single_sample/UltimaGenomics/BroadInternalUltimaGenomics.changelog.md
@@ -1,3 +1,8 @@
+# 1.1.3
+2024-12-05 (Date of Last Commit)
+
+* Updated the name of the output for ReblockGVCFs; this does not affect this pipeline
+
 # 1.1.2
 2024-11-04 (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 = "1.1.2"
+  String pipeline_version = "1.1.3"
 
   input {
 

diff --git a/verification/test-wdls/TestReblockGVCF.wdl b/verification/test-wdls/TestReblockGVCF.wdl
@@ -54,8 +54,8 @@ workflow TestReblockGVCF {
     # Collect all of the pipeline outputs into single Array[String]
     Array[String] pipeline_outputs = flatten([
                                     [ # File outputs
-                                    ReblockGVCF.output_vcf_index,
-                                    ReblockGVCF.output_vcf,
+                                    ReblockGVCF.reblocked_gvcf_index,
+                                    ReblockGVCF.reblocked_gvcf,
                                     ],
 
     ])
@@ -86,13 +86,13 @@ workflow TestReblockGVCF {
     if (!update_truth){
         call Utilities.GetValidationInputs as GetGvcf {
           input:
-            input_file = ReblockGVCF.output_vcf,
+            input_file = ReblockGVCF.reblocked_gvcf,
             results_path = results_path,
             truth_path = truth_path
         }
         call Utilities.GetValidationInputs as GetGvcfIndex {
           input:
-            input_file = ReblockGVCF.output_vcf_index,
+            input_file = ReblockGVCF.reblocked_gvcf_index,
             results_path = results_path,
             truth_path = truth_path
         }
-Original file line number
+Diff line change
@@ Expand Up @@
     workflow BroadInternalUltimaGenomics {
-      String pipeline_version = "1.1.2"
+      String pipeline_version = "1.1.3"
       input {
@@ Expand Down @@