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dev --> staging #1491

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Jan 29, 2025
Merged

dev --> staging #1491

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50 changes: 25 additions & 25 deletions pipeline_versions.txt
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Original file line number Diff line number Diff line change
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Pipeline Name Version Date of Last Commit
ExomeReprocessing 3.3.3 2024-11-04
CramToUnmappedBams 1.1.3 2024-08-02
IlluminaGenotypingArray 1.12.24 2024-11-04
WholeGenomeReprocessing 3.3.3 2024-11-04
ExternalExomeReprocessing 3.3.3 2024-11-04
ExternalWholeGenomeReprocessing 2.3.3 2024-11-04
UltimaGenomicsJointGenotyping 1.2.2 2024-11-04
ReblockGVCF 2.4.0 2024-12-05
JointGenotypingByChromosomePartOne 1.5.2 2024-11-04
JointGenotypingByChromosomePartTwo 1.5.2 2024-11-04
JointGenotyping 1.7.2 2024-11-04
ExomeGermlineSingleSample 3.2.3 2024-11-04
ExternalExomeReprocessing 3.3.3 2024-11-04
CramToUnmappedBams 1.1.3 2024-08-02
ExomeReprocessing 3.3.3 2024-11-04
GDCWholeGenomeSomaticSingleSample 1.3.4 2024-11-04
UltimaGenomicsWholeGenomeCramOnly 1.0.23 2024-11-04
WholeGenomeGermlineSingleSample 3.3.3 2024-11-04
UltimaGenomicsWholeGenomeGermline 1.1.3 2024-12-05
ExomeGermlineSingleSample 3.2.3 2024-11-04
JointGenotyping 1.7.2 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
VariantCalling 2.2.4 2024-11-04
GDCWholeGenomeSomaticSingleSample 1.3.4 2024-11-04
UltimaGenomicsWholeGenomeCramOnly 1.0.23 2024-11-04
IlluminaGenotypingArray 1.12.24 2024-11-04
AnnotationFiltration 1.2.7 2024-11-04
CheckFingerprint 1.0.22 2024-10-28
ValidateChip 1.16.7 2024-11-04
Imputation 1.1.15 2024-11-04
MultiSampleArrays 1.6.2 2024-08-02
Arrays 2.6.30 2024-11-04
RNAWithUMIsPipeline 1.0.18 2024-11-04
BroadInternalUltimaGenomics 1.1.3 2024-12-05
BroadInternalRNAWithUMIs 1.0.36 2024-11-04
BroadInternalImputation 1.1.14 2024-11-04
BroadInternalArrays 1.1.14 2024-11-04
BroadInternalRNAWithUMIs 1.0.36 2024-11-04
RNAWithUMIsPipeline 1.0.18 2024-11-04
Imputation 1.1.15 2024-11-04
MultiSampleArrays 1.6.2 2024-08-02
ValidateChip 1.16.7 2024-11-04
Arrays 2.6.30 2024-11-04
AnnotationFiltration 1.2.7 2024-11-04
Multiome 5.9.6 2025-01-21
MultiSampleSmartSeq2SingleNucleus 2.0.7 2025-01-13
BuildIndices 4.0.0 2025-01-17
snm3C 4.0.4 2024-08-06
SlideSeq 3.4.8 2025-01-13
PairedTag 1.10.0 2025-01-21
atac 2.6.0 2025-01-21
scATAC 1.3.2 2023-08-03
snm3C 4.0.4 2024-08-06
Optimus 7.9.1 2025-01-13
BuildIndices 4.0.0 2025-01-17
MultiSampleSmartSeq2 2.2.22 2024-09-11
Optimus 7.9.1 2025-01-13
atac 2.6.0 2025-01-21
PairedTag 1.10.0 2025-01-21
SmartSeq2SingleSample 5.1.21 2024-09-11
MultiSampleSmartSeq2SingleNucleus 2.0.7 2025-01-13
2 changes: 1 addition & 1 deletion pipelines/skylab/paired_tag/PairedTag.changelog.md
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* Added a boolean variable is_slidetags; default is false, but set to true if Slide-Tags pipeline is calling Optimus
* Added reference_gtf_file to the output h5ad unstructured metadata
* Added the fragment file CSI index as workflow output
* Updated the default STARsolo multimapping parameter to the "EM" tehcnique
* Updated the default STARsolo multimapping parameter to the EM tehcnique

# 1.9.0
2024-12-05 (Date of Last Commit)
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