Merge pull request #1701 from broadinstitute/TSPS-621_imputation_qc_messages

TSPS-621 Update ArrayImputationQC WDL's QcChecks task with clearer messages

Author: mmorgantaylor

pipeline_versions.txt

@@ -1,12 +1,12 @@
-ArrayImputationQC	 1.2.2	2025-10-07 
+ArrayImputationQC	 1.2.3 	2025-10-17 
 ArrayImputationQuotaConsumed	 1.1.0	2025-09-29 
 BuildIndices	 5.0.0	2025-09-30 
 CramToUnmappedBams	 1.1.3	2024-08-02 
 ExomeGermlineSingleSample	 3.2.6	2025-10-09 
 ExomeReprocessing	 3.3.6	2025-10-09 
 IlluminaGenotypingArray	 1.12.26	2025-10-09 
 Imputation	 1.1.23	2025-10-03 
-ImputationBeagle	 2.2.3	2025-10-07 
+ImputationBeagle	 2.2.4	2025-10-17 
 JointGenotyping	 1.7.3	2025-08-11 
 MultiSampleSmartSeq2SingleNucleus	 2.2.2	 2025-06-20 
 Multiome	 6.1.3	2025-08-15 

pipelines/wdl/arrays/imputation_beagle/ImputationBeagle.changelog.md

@@ -1,3 +1,8 @@
+# 2.2.4
+2025-10-17 (Date of Last Commit)
+
+* Update input_qc_version to 1.2.3 to match latest changes in InputQC wdl
+
 # 2.2.3
 2025-10-07 (Date of Last Commit)
 

pipelines/wdl/arrays/imputation_beagle/ImputationBeagle.wdl

@@ -5,8 +5,8 @@ import "../../../../tasks/wdl/ImputationTasks.wdl" as tasks
 import "../../../../tasks/wdl/ImputationBeagleTasks.wdl" as beagleTasks
 
 workflow ImputationBeagle {
-  String pipeline_version = "2.2.3"
-  String input_qc_version = "1.2.2"
+  String pipeline_version = "2.2.4"
+  String input_qc_version = "1.2.3"
   String quota_consumed_version = "1.1.0"
 
   input {

pipelines/wdl/arrays/imputation_beagle/input_qc/ArrayImputationQC.changelog.md

@@ -1,3 +1,8 @@
+# 1.2.3 
+2025-10-17 (Date of Last Commit)
+
+* Update QcChecks task to improve error messages.
+
 # 1.2.2
 2025-10-07 (Date of Last Commit)
 
@@ -6,7 +11,7 @@
 # 1.2.1
 2025-10-01 (Date of Last Commit)
 
-* Add check for vcf being bgzipped and in sorted order
+* Add check for vcf being bgzipped and in sorted order.
 
 # 1.2.0
 2025-09-29 (Date of Last Commit)
@@ -21,12 +26,12 @@
 # 1.0.3
 2025-09-15 (Date of Last Commit)
 
-* Add instruction for updating ImputationBeagle wdl when this workflow's pipeline_version changes for improved version tracking across wdls
+* Add instruction for updating ImputationBeagle wdl when this workflow's pipeline_version changes for improved version tracking across wdls.
 
 # 1.0.2
 2025-09-03 (Date of Last Commit)
 
-* Add optional pipeline_header_line input to match beagle imputation pipeline inputs
+* Add optional pipeline_header_line input to match beagle imputation pipeline inputs.
 
 # 1.0.1
 2025-08-26 (Date of Last Commit)

pipelines/wdl/arrays/imputation_beagle/input_qc/ArrayImputationQC.wdl

@@ -4,7 +4,7 @@ import "../../../../../tasks/wdl/ImputationBeagleQcTasks.wdl" as tasks
 
 workflow InputQC {
     # if this changes, update the input_qc_version value in ImputationBeagle.wdl
-    String pipeline_version = "1.2.2"
+    String pipeline_version = "1.2.3"
 
 
     input {