v0.17.2-beta

Updates include:

• Documentation updates
• Subdivide FilterBatch into three workflows to enable choice of IQR cutoff

v0.17.1-beta

Quick fix for v0.17-beta - renaming trainGCNV to TrainGCNV consistently

v0.17-beta

Updates include:

• Rename pipeline modules with descriptive names
• Run metrics workflows as part of main workflows for debugging info and ease of testing
• For Terra, add single-batch configs for cohort-level steps

v0.16-beta

Updates include:

• PEP8 linting of all python scripts
• Fix bug in svtest
• Allow missing samples for BAF collection from joint VCF or gVCFs in Module00c
• Add VCF indexes to Module04b outputs to work with cromwell workflow outputs bucket

v0.15.1-beta

Add option to provide file containing list of GCS paths to SNP VCF shards in Module00c because Terra has a limit on array length in inputs

v0.15-beta-hotfix

Hotfix for Tasks0506.wdl cromwell compliance

v0.15-beta

Changes include:

• Bug fix in a CleanVCF script
• Evaluation of additional variants in Module04b
• Enable easier skipping of Melt for Terra
• Generate median coverage files in Module00b for batching
• Reduce memory when merging genotypes in TrainRDGenotyping
• Support original sample IDs in snp_vcfs in Module00c

v0.14.3-beta

Includes bug fix for Module04b

v0.14.2-beta

Changes include:

• Bug fixes to RDTest, affecting Module02 and Module04

v0.14.1-beta: Minor updates to v0.14-beta

Changes include:

• Option to revise all non-canonical bases in BAM file to N during CramToBam (not recommended by default, as it is not optimized yet and will cost more)
• Reduce default disk for Module02 test tasks
• Remove old WDL headers
• Fix bug in CleanVcf that occurred when a sample ID appeared in a batch/variant ID
• Make read length input to CollectWgsMetrics for MELT in case read length differs from default 150bp