WARP versions of pipelines depending on StarAlign

Author: rsc3

pipeline_versions.txt

@@ -9,16 +9,16 @@ IlluminaGenotypingArray	 1.12.27	2026-01-21
 Imputation	 1.1.23	2025-10-03 
 ImputationBeagle	 3.0.1	2026-02-23 
 JointGenotyping	 1.7.3	2025-08-11 
-MultiSampleSmartSeq2SingleNucleus	 2.2.5	2026-02-24 
-Multiome	 6.1.5	2026-02-24 
+MultiSampleSmartSeq2SingleNucleus	 2.2.6	2026-03-31 
+Multiome	 6.1.6	2026-03-31 
 Optimus	 8.0.7	2026-03-31 
-PairedTag	 2.1.11	2026-02-24 
+PairedTag	 2.1.12	2026-03-31 
 PeakCalling	 1.0.1	2025-08-11 
 Pipeline Name	Version	Date of Last Commit
 RNAWithUMIsPipeline	 1.0.20	2026-01-21 
 ReblockGVCF	 2.4.4	2026-01-29 
 SlideSeq	 3.6.6	2026-03-31 
-SlideTags	 1.0.8	2026-02-24 
+SlideTags	 1.0.9	2026-03-31 
 UltimaGenomicsJointGenotyping	 1.2.3	2025-08-11 
 UltimaGenomicsWholeGenomeCramOnly	 1.1.3	2026-01-21 
 UltimaGenomicsWholeGenomeGermline	 1.2.2	2026-01-29 

pipelines/wdl/multiome/Multiome.changelog.md

@@ -1,3 +1,8 @@
+# 6.1.6
+2026-03-31 (Date of Last Commit)
+
+* Updated Optimus sub-workflow to v8.0.7 which moved conditional logic for STAR parameters out of task command blocks into workflow-level WDL expressions; this does not affect the outputs of this pipeline
+
 # 6.1.5
 2026-02-24 (Date of Last Commit)
 

pipelines/wdl/multiome/Multiome.wdl

@@ -10,7 +10,7 @@ import "../../../tasks/wdl/Utilities.wdl" as utils
 workflow Multiome {
 
 
-    String pipeline_version = "6.1.5"
+    String pipeline_version = "6.1.6"
 
 
     input {

pipelines/wdl/paired_tag/PairedTag.changelog.md

@@ -1,3 +1,8 @@
+# 2.1.12
+2026-03-31 (Date of Last Commit)
+
+* Updated Optimus sub-workflow to v8.0.7 which moved conditional logic for STAR parameters out of task command blocks into workflow-level WDL expressions; this does not affect the outputs of this pipeline
+
 # 2.1.11
 2026-02-24 (Date of Last Commit)
 

pipelines/wdl/paired_tag/PairedTag.wdl

@@ -9,7 +9,7 @@ import "../../../tasks/wdl/Utilities.wdl" as utils
 
 workflow PairedTag {
 
-    String pipeline_version = "2.1.11"
+    String pipeline_version = "2.1.12"
 
     input {
         String input_id

pipelines/wdl/slidetags/SlideTags.changelog.md

@@ -1,3 +1,8 @@
+# 1.0.9
+2026-03-31 (Date of Last Commit)
+
+* Updated Optimus sub-workflow to v8.0.7 which moved conditional logic for STAR parameters out of task command blocks into workflow-level WDL expressions; this does not affect the outputs of this pipeline
+
 # 1.0.8
 2026-02-24 (Date of Last Commit)
 

pipelines/wdl/slidetags/SlideTags.wdl

@@ -6,7 +6,7 @@ import "../optimus/Optimus.wdl" as optimus
 
 workflow SlideTags {
 
-    String pipeline_version = "1.0.8"
+    String pipeline_version = "1.0.9"
 
     input {
 

pipelines/wdl/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md

@@ -1,3 +1,8 @@
+# 2.2.6
+2026-03-31 (Date of Last Commit)
+
+* Updated StarAlign.wdl dependency which refactored task inputs and added a new ParseReadStructure utility task; the tasks used by this pipeline (StarAlignFastqMultisample, STARGenomeRefVersion) are unchanged and this does not affect the outputs of this pipeline
+
 # 2.2.5
 2026-02-24 (Date of Last Commit)
 

pipelines/wdl/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.wdl

@@ -59,7 +59,7 @@ workflow MultiSampleSmartSeq2SingleNucleus {
   }
 
   # Version of this pipeline
-  String pipeline_version = "2.2.5"
+  String pipeline_version = "2.2.6"
 
   if (false) {
      String? none = "None"