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

v0.14-beta

Updated pre-release of cohort pipeline for Terra. Changes include:

• Switch to single cohort-level ped file rather than batch ped files
• Add functionality to randomly subsample input samples in trainGCNV
• Bug fixes to FORMAT EV field
• Updates to Module07-Module10

v0.13.1-beta Minor updates to v0.13-beta

• Fixes to Module07
• Minor changes to re-genotype filtering in Module04b for smaller cohorts

v0.13-beta

Updated pre-release of batch pipeline for Terra, incorporating changes such as:

• Make outlier cutoff table input to Module03 optional to better reflect use case
• Bug fixes and performance improvements to Module04b
• Break-up of Module0506 into sub-workflows
• Fix handling of MEI SVTYPE in Module07
• Changes reflected in v0.12-beta release

v0.12-beta

This release upgrades the single sample pipeline to work with the upgrades to gCNV and median-based re-genotyping that were implemented in the joint pipeline. Other changes include:

• Generates input JSON files and the single-sample pipeline Terra workspace files from templates
• Allows optional inputs of precomputed module00a files for the single sample pipeline
• Bug fixes for module 03 and MasterVcfQC
• Improved resource acquisition and monitoring scripts
• Implements a sample wide QC step in the single sample pipeline for samples that are outliers in coverage or WGD score