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

atac_v2.5.3

2.5.3

2024-11-22 (Date of Last Commit)

• Updated the warp-tools docker; this update changes the way gene_names are identified when creating gene expression h5ad files; does not impact ATAC workflow

SlideSeq_v3.4.7

3.4.7

2024-12-3 (Date of Last Commit)

• Fixed a bug in the StarSoloFastq task that caused the pipeline to not output a UniqueAndMult-Uniform.mtx when --soloMultiMappers Uniform was passed to STAR; this does not affect the outputs of the pipeline