diff --git a/pipeline_versions.txt b/pipeline_versions.txt
index f7dfdd8c4a..1efe91457c 100644
--- a/pipeline_versions.txt
+++ b/pipeline_versions.txt
@@ -1,42 +1,42 @@
 Pipeline Name	Version	Date of Last Commit
-RNAWithUMIsPipeline	 1.0.17	2024-09-06 
-CheckFingerprint	 1.0.21	2024-09-06 
-CramToUnmappedBams	 1.1.3	2024-08-02 
-ExomeReprocessing	 3.3.1	2024-09-17 
-ExternalExomeReprocessing	 3.3.1	2024-09-17 
-ExternalWholeGenomeReprocessing	 2.3.1	2024-09-17 
-WholeGenomeReprocessing	 3.3.1	2024-09-17 
-AnnotationFiltration	 1.2.6	2024-09-06 
-IlluminaGenotypingArray	 1.12.22	2024-09-06 
-UltimaGenomicsWholeGenomeGermline	 1.1.0	2024-09-06 
-ExomeGermlineSingleSample	 3.2.1	2024-09-17 
-WholeGenomeGermlineSingleSample	 3.3.1	2024-09-17 
-JointGenotypingByChromosomePartTwo	 1.5.1	2024-09-10 
-JointGenotypingByChromosomePartOne	 1.5.1	2024-09-10 
-ReblockGVCF	 2.3.0	2024-09-06 
-JointGenotyping	 1.7.1	2024-09-10 
-UltimaGenomicsJointGenotyping	 1.2.1	2024-09-10 
-VariantCalling	 2.2.2	2024-09-06 
-UltimaGenomicsWholeGenomeCramOnly	 1.0.21	2024-09-06 
-GDCWholeGenomeSomaticSingleSample	 1.3.3	2024-09-06 
-Imputation	 1.1.14	2024-09-06 
-Arrays	 2.6.28	2024-09-06 
-MultiSampleArrays	 1.6.2	2024-08-02 
-ValidateChip	 1.16.6	2024-09-06 
-BroadInternalRNAWithUMIs	 1.0.34	2024-09-06 
-BroadInternalUltimaGenomics	 1.1.0	2024-09-06 
-BroadInternalImputation	 1.1.13	2024-09-06 
-BroadInternalArrays	 1.1.12	2024-09-06 
-MultiSampleSmartSeq2	 2.2.22	2024-09-11 
 MultiSampleSmartSeq2SingleNucleus	 2.0.0	2024-09-11 
+MultiSampleSmartSeq2	 2.2.22	2024-09-11 
 PairedTag	 1.6.1	2024-09-11 
-SmartSeq2SingleSample	 5.1.21	2024-09-11 
-scATAC	 1.3.2	2023-08-03 
 Optimus	 7.6.1	2024-09-11 
-Multiome	 5.6.1	2024-09-11 
+atac	 2.3.1	2024-09-11 
 snm3C	 4.0.4	2024-08-06 
+SmartSeq2SingleSample	 5.1.21	2024-09-11 
+Multiome	 5.6.1	2024-09-11 
+scATAC	 1.3.2	2023-08-03 
 BuildIndices	 3.0.0	2023-12-06 
-atac	 2.3.1	2024-09-11 
 SlideSeq	 3.4.1	2024-09-11 
 BuildCembaReferences	 1.0.0	2020-11-15 
 CEMBA	 1.1.7	2024-09-06 
+GDCWholeGenomeSomaticSingleSample	 1.3.3	2024-09-06 
+UltimaGenomicsWholeGenomeCramOnly	 1.0.21	2024-09-06 
+JointGenotypingByChromosomePartOne	 1.5.1	2024-09-10 
+JointGenotypingByChromosomePartTwo	 1.5.1	2024-09-10 
+UltimaGenomicsJointGenotyping	 1.2.1	2024-09-10 
+JointGenotyping	 1.7.1	2024-09-10 
+ReblockGVCF	 2.3.0	2024-09-06 
+VariantCalling	 2.2.2	2024-09-06 
+WholeGenomeGermlineSingleSample	 3.3.1	2024-09-17 
+UltimaGenomicsWholeGenomeGermline	 1.1.0	2024-09-06 
+ExomeGermlineSingleSample	 3.2.1	2024-09-17 
+ValidateChip	 1.16.6	2024-09-06 
+Arrays	 2.6.28	2024-09-06 
+Imputation	 1.1.14	2024-09-06 
+MultiSampleArrays	 1.6.2	2024-08-02 
+BroadInternalUltimaGenomics	 1.1.0	2024-09-06 
+BroadInternalArrays	 1.1.12	2024-09-06 
+BroadInternalImputation	 1.1.13	2024-09-06 
+BroadInternalRNAWithUMIs	 1.0.34	2024-09-06 
+CramToUnmappedBams	 1.1.3	2024-08-02 
+ExternalWholeGenomeReprocessing	 2.3.1	2024-09-17 
+ExternalExomeReprocessing	 3.3.1	2024-09-17 
+WholeGenomeReprocessing	 3.3.1	2024-09-17 
+ExomeReprocessing	 3.3.1	2024-09-17 
+IlluminaGenotypingArray	 1.12.22	2024-09-06 
+CheckFingerprint	 1.0.21	2024-09-06 
+AnnotationFiltration	 1.2.6	2024-09-06 
+RNAWithUMIsPipeline	 1.0.17	2024-09-06