NP address intermittent failures in new testing framework (#1517)

* address intermittent failures

* Updated pipeline_versions.txt with all pipeline version information

---------

Co-authored-by: GitHub Action <action@github.com>

Author: nikellepetrillo

pipeline_versions.txt

@@ -1,40 +1,40 @@
 Pipeline Name	Version	Date of Last Commit
-snm3C	 4.0.4	2024-08-06 
-BuildIndices	 4.0.0	2025-01-17 
-scATAC	 1.3.2	2023-08-03 
-MultiSampleSmartSeq2SingleNucleus	 2.0.8	2025-02-25 
-atac	 2.7.1	2025-02-25 
-Optimus	 7.9.2	2025-02-25 
-SmartSeq2SingleSample	 5.1.21	2024-09-11 
-Multiome	 5.11.0	2025-02-25 
-PairedTag	 1.10.2 	2025-02-25 
-SlideSeq	 3.4.9	2025-02-25 
-MultiSampleSmartSeq2	 2.2.22	2024-09-11 
-AnnotationFiltration	 1.2.7	2024-11-04 
-RNAWithUMIsPipeline	 1.0.18	2024-11-04 
-Imputation	 1.1.15	2024-11-04 
 Arrays	 2.6.30	2024-11-04 
-MultiSampleArrays	 1.6.2	2024-08-02 
 ValidateChip	 1.16.7	2024-11-04 
-JointGenotyping	 1.7.2	2024-11-04 
+Imputation	 1.1.15	2024-11-04 
+MultiSampleArrays	 1.6.2	2024-08-02 
+WholeGenomeReprocessing	 3.3.3	2024-11-04 
+ExomeReprocessing	 3.3.3	2024-11-04 
+CramToUnmappedBams	 1.1.3	2024-08-02 
+ExternalWholeGenomeReprocessing	 2.3.3	2024-11-04 
+ExternalExomeReprocessing	 3.3.3	2024-11-04 
+BroadInternalArrays	 1.1.14	2024-11-04 
+BroadInternalImputation	 1.1.14	2024-11-04 
+BroadInternalRNAWithUMIs	 1.0.36	2024-11-04 
+BroadInternalUltimaGenomics	 1.1.3	2024-12-05 
+RNAWithUMIsPipeline	 1.0.18	2024-11-04 
+IlluminaGenotypingArray	 1.12.24	2024-11-04 
+AnnotationFiltration	 1.2.7	2024-11-04 
+UltimaGenomicsWholeGenomeCramOnly	 1.0.23	2024-11-04 
+GDCWholeGenomeSomaticSingleSample	 1.3.4	2024-11-04 
+UltimaGenomicsWholeGenomeGermline	 1.1.3	2024-12-05 
+WholeGenomeGermlineSingleSample	 3.3.3	2024-11-04 
+ExomeGermlineSingleSample	 3.2.3	2024-11-04 
+VariantCalling	 2.2.4	2024-11-04 
 ReblockGVCF	 2.4.0	2024-12-05 
 UltimaGenomicsJointGenotyping	 1.2.2	2024-11-04 
-JointGenotypingByChromosomePartTwo	 1.5.2	2024-11-04 
 JointGenotypingByChromosomePartOne	 1.5.2	2024-11-04 
-ExomeGermlineSingleSample	 3.2.3	2024-11-04 
-WholeGenomeGermlineSingleSample	 3.3.3	2024-11-04 
-UltimaGenomicsWholeGenomeGermline	 1.1.3	2024-12-05 
-VariantCalling	 2.2.4	2024-11-04 
-GDCWholeGenomeSomaticSingleSample	 1.3.4	2024-11-04 
-UltimaGenomicsWholeGenomeCramOnly	 1.0.23	2024-11-04 
+JointGenotypingByChromosomePartTwo	 1.5.2	2024-11-04 
+JointGenotyping	 1.7.2	2024-11-04 
 CheckFingerprint	 1.0.22	2024-10-28 
-BroadInternalRNAWithUMIs	 1.0.36	2024-11-04 
-BroadInternalImputation	 1.1.14	2024-11-04 
-BroadInternalArrays	 1.1.14	2024-11-04 
-BroadInternalUltimaGenomics	 1.1.3	2024-12-05 
-IlluminaGenotypingArray	 1.12.24	2024-11-04 
-ExternalExomeReprocessing	 3.3.3	2024-11-04 
-ExternalWholeGenomeReprocessing	 2.3.3	2024-11-04 
-ExomeReprocessing	 3.3.3	2024-11-04 
-CramToUnmappedBams	 1.1.3	2024-08-02 
-WholeGenomeReprocessing	 3.3.3	2024-11-04 
+scATAC	 1.3.2	2023-08-03 
+MultiSampleSmartSeq2	 2.2.22	2024-09-11 
+BuildIndices	 4.0.0	2025-01-17 
+SlideSeq	 3.4.9	2025-02-25 
+PairedTag	 1.10.2 	2025-02-25 
+MultiSampleSmartSeq2SingleNucleus	 2.0.8	2025-02-25 
+atac	 2.7.1	2025-02-25 
+snm3C	 4.0.4	2024-08-06 
+SmartSeq2SingleSample	 5.1.21	2024-09-11 
+Optimus	 7.9.2	2025-02-25 
+Multiome	 5.11.0	2025-02-25