SlideTags_v1.0.5

2025-10-24 (Date of Last Commit)

• Updated the positioning.wdl code to the latest version from the Macosko Lab repository to incorporate recent improvements

ImputationBeagle_v2.2.4

2.2.4

2025-10-17 (Date of Last Commit)

• Update input_qc_version to 1.2.3 to match latest changes in InputQC wdl

ArrayImputationQC_v1.2.3

1.2.3

2025-10-17 (Date of Last Commit)

• Update QcChecks task to improve error messages.

SlideTags_develop

1.0.5

2025-10-24 (Date of Last Commit)

• Updated the positioning.wdl code to the latest version from the Macosko Lab repository to incorporate recent improvements

MultiSampleSmartSeq2_develop

2.2.23

2025-03-06 (Date of Last Commit)

• The MultiSampleSmartSeq2 pipeline is now deprecated

BuildIndices_v5.0.0

5.0.0

2025-09-30 (Date of Last Commit)

• Added the MitoAnnotate task to optionally append mitochondrial sequence and annotations via MitoFinder.
  This task runs early in the pipeline and updates the genome FASTA and GTF prior to building STAR and BWA indices.

ImputationBeagle_develop

2.2.4

2025-10-17 (Date of Last Commit)

• Update input_qc_version to 1.2.3 to match latest changes in InputQC wdl

BuildIndices_develop

5.0.0

2025-09-30 (Date of Last Commit)

• Added the MitoAnnotate task to optionally append mitochondrial sequence and annotations via MitoFinder.
  This task runs early in the pipeline and updates the genome FASTA and GTF prior to building STAR and BWA indices.

ArrayImputationQC_develop

1.2.3

2025-10-17 (Date of Last Commit)

• Update QcChecks task to improve error messages.

WholeGenomeReprocessing_v3.3.6

3.3.6

2025-10-09 (Date of Last Commit)

• Modified the ReblockGVCF.wdl to use bash's basename instead of WDL's basename; this does not affect the outputs of this pipeline