atac_v2.7.1

2.7.1

2025-02-25 (Date of Last Commit)

• Added a new warning for peak calling step if the probability_threshold is too low, resutling in a null matrix after doublet filtering
• Updated the probability threshold default to 0.5
• 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

SlideSeq_v3.4.9

3.4.9

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 workflows; this does not impact Slideseq

PairedTag_v1.10.2

1.10.2

2025-02-25 (Date of Last Commit)

• Updated the SnapATAC2 docker image to the latest SnapATAC2, allowing for future peak calling implementation
• 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 headers

Optimus_v7.9.2

7.9.2

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

Multiome_v5.11.0

5.11.0

2025-02-25 (Date of Last Commit)

• Refactored the Peak Calling step of Multiome to use the JoinBarcodes output h5ad as the input for peak calling, ensuring the h5ad files have both GEX and ATAC barcodes
• 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 headers

MultiSampleSmartSeq2SingleNucleus_v2.0.8

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

Imputation_v1.1.16

1.1.16

2025-02-24 (Date of Last Commit)

• Updated runtime parameters in some ImputationTasks, and added an explicit definition of a vcf_index.

ImputationBeagle_v1.0.0

1.0.0

2025-02-26 (Date of Last Commit)

• Initial public release of the ImputationBeagle pipeline.
  • The ImputationBeagle pipeline imputes missing genotypes from a multi-sample VCF using a large genomic reference panel. It is based on the Michigan Imputation Server pipeline but uses the Beagle imputation tool instead of minimac. Overall, the pipeline filters, phases, and performs imputation on a multi-sample VCF. It outputs the imputed VCF.

BroadInternalImputation_v1.1.15

1.1.15

2025-02-24 (Date of Last Commit)

• Updated runtime parameters in some ImputationTasks, and added an explicit definition of a vcf_index.

ArrayImputationQuotaConsumed_v1.0.0

1.0.0

2025-02-24 (Date of Last Commit)

• Initial release of pipeline to calculate the number of samples, i.e. quota used by an imputation service that uses ImputationBeagle.wdl.