atac_develop

2.4.0

2024-10-23 (Date of Last Commit)

• Added a new input parameter for atac_expected_cells, which describes the numnber of cells used for the library preparation
• Updated the ATAC library CSV to be consistent in file naming convention and to have similar case for metric names to the Optimus workflow library CSV
• Added a new metric to the ATAC library CSV to calculate percent_target, which is the number of estimated cells by SnapATAC2 divided by expected_cells input
• Updated the ATAC workflow so that the output fragment file is bgzipped by default

WholeGenomeReprocessing_develop

3.3.2

2024-10-28 (Date of Last Commit)

• Updated the docker in the ValidateVCF task; this does not affect this pipeline

WholeGenomeGermlineSingleSample_develop

3.3.2

2024-10-28 (Date of Last Commit)

• Updated the docker in the ValidateVCF task; this does not affect this pipeline

VariantCalling_develop

2.2.3

2024-10-28 (Date of Last Commit)

• Updated the docker in the ValidateVCF task; this does not affect this pipeline

UltimaGenomicsWholeGenomeGermline_develop

1.1.1

2024-10-28 (Date of Last Commit)

• Updated the docker in the ValidateVCF task; this does not affect this pipeline

UltimaGenomicsWholeGenomeCramOnly_develop

1.0.22

2024-10-28 (Date of Last Commit)

• Updated the docker in the ValidateVCF task; this does not affect this pipeline

SlideSeq_develop

3.4.3

2024-10-24 (Date of Last Commit)

• Updated the h5adUtils WDL to rename the gene expression library CSV filename; this does not impact slideseq
• Updated the ATAC fragment file output so that it is bgzipped; this does not impact the slideseq workflow

ReblockGVCF_develop

2.3.1

2024-10-28 (Date of Last Commit)

• Updated GATK for Validate Variants, which reduces the memory requirements for the task when an interval list is not provided

PairedTag_develop

1.8.0

2024-10-23 (Date of Last Commit)

• Updated the workflow to include a new expected_cells input parameter describing the number of cells used as input to the library preparation; this is passed to both the ATAC workflows and Optimus workflows and the default is set to 3000 cells
• Updated the ATAC library CSV and the Gene Expression library CSV to be consistent in file naming convention and to have similar case for metric names
• Added a new metric to the ATAC library CSV to calculate percent_target, which is the number of estimated cells by SnapATAC2 divided by expected_cells input
• Updated the ATAC fragment file output so that it is bgzipped

Optimus_develop

7.8.0

2024-10-23 (Date of Last Commit)

• Renamed the input expected_cells to gex_expected_cells
• Updated gex_expected_cells to a required output
• Reformatted the library CSV output filename to remove an extra gex
• Updated the ATAC fragment file output so that it is bgzipped; this does not impact the Optimus workflow