MultiSampleSmartSeq2SingleNucleus_develop

2.0.8

2025-02-25 (Date of Last Commit)

• Updated the warp-tools docker image to include an update to the GroupQCs function in sctools; this does not affect the outputs of the pipeline
• Added reference information to the BAM header for Optimus and ATAC; does not impact snSS2

atac_v2.7.0

2.7.0

2025-02-03 (Date of Last Commit)

• Added an optional PeakCalling task
• Added a boolean variable peak_calling; default is false

PairedTag_v1.10.1

1.10.1

2025-02-03 (Date of Last Commit)

• Added an optional PeakCalling task to the ATAC workflow; this does not affect the outputs of the pipeline
• Added a boolean variable run_peak_calling to the Multiome pipeline; default is false and this does not affect the outputs of the pipeline

Multiome_v5.10.0

5.10.0

2025-02-03 (Date of Last Commit)

• Added an optional PeakCalling task to the ATAC workflow
• Added a boolean variable run_peak_calling to the Multiome pipeline; default is false

atac_v2.6.0

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

UltimaGenomicsWholeGenomeGermline_v1.1.3

1.1.3

2024-12-05 (Date of Last Commit)

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

SlideSeq_v3.4.8

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

ReblockGVCF_v2.4.0

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

Optimus_v7.9.1

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

Multiome_v5.9.6

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