atac_develop

2.6.0

2025-01-21 (Date of Last Commit)

• Added reference_gtf_file to the output h5ad unstructured metadata
• Added the fragment file CSI index as a workflow output

Multiome_develop

5.9.6

2025-01-21 (Date of Last Commit)

• Added a boolean variable is_slidetags; default is false but it is set to true if the Slide-Tags pipeline is calling Optimus
• Added reference_gtf_file to the output h5ad unstructured metadata
• Added the ATAC fragment file CSI index as high-level ATAC workflow output; this does not impact the Multiome workflow as Multiome already produces the csi index from ATAC

BuildIndices_develop

4.0.0

2025-01-17 (Date of Last Commit)

• Updated the WDL to include a new docker version 2.1.0 which has new python scripts for handling a custom marmoset GTF input
• Updated the WDL to run new marmoset scripts if the organism input is set to marmoset

SlideSeq_develop

3.4.8

2025-01-13 (Date of Last Commit)

• Added a boolean variable is_slidetags; this does not affect the outputs of the pipeline
• Added reference_gtf_file to the output h5ad unstructured metadata

Optimus_develop

7.9.1

2025-01-13 (Date of Last Commit)

• Added a boolean variable is_slidetags; set to false by default, but set to true if the Slide-Tags pipeline is calling Optimus

• Added reference_gtf_file to the output h5ad unstructured metadata

MultiSampleSmartSeq2SingleNucleus_develop

2.0.7

2025-01-13 (Date of Last Commit)

• Added a boolean variable is_slidetags; this does not affect the outputs of the pipeline
• Added reference_gtf_file to the output h5ad unstructured metadata

ImputationBeagle_development_v0.0.3

TSPS-341 remove tasks for recovering variants not in the reference pa…

UltimaGenomicsWholeGenomeGermline_develop

1.1.3

2024-12-05 (Date of Last Commit)

• Updated the name of the output for ReblockGVCFs; this does not affect this pipeline

ReblockGVCF_develop

2.4.0

2024-12-05 (Date of Last Commit)

• Updated output names for ReblockGVCF workflow from output_vcf and output_vcf_index to reblocked_gvcf and reblocked_gvcf_index respectively

BroadInternalUltimaGenomics_develop

1.1.3

2024-12-05 (Date of Last Commit)

• Updated the name of the output for ReblockGVCFs; this does not affect this pipeline