broadinstitute/gatk-sv: v0.28.5-beta

Updates

GatherSampleEvidence

• Copy or move the files instead of creating symlinks in the LocalizeReads task for compatibility with CoA/TES
• Make LocalizeReads optional
• Make manta region bed index required
• Make MELT scripts independent of the execution path

Main pipeline

• Rewrite SplitVariants in TasksGenotypeBatch.wdl
• Disable MakeCohortVcfMetrics by default
• Find CN field for mCNVs in MainVcfQc without hard-coding order of format fields
• Update BEDTools version to 2.31.0
• Two small bugfixes to EvidenceQc
• Update gatk_docker with CPX annotation changes to SVAnnotate
• Reduce redundant docker image inputs: sv_pipeline_base_docker, sv_pipeline_hail_docker, sv_pipeline_updates_docker, sv_pipeline_rdtest_docker all now just sv_pipeline_docker

Downstream filtering

• Reduce SVConcordance memory usage
• Release AoU filtering model
• Make the ploidy table a workflow output instead of an intermediate
• Change Vapor bed preprocessing errors to warnings
• Genotype filtering training labels and cutoff optimization

Misc.

• Add ReshardVcf workflow
• Setup automatic updates to WDLs on Dockstore
• Trivial change to sv-pipeline-virtual-env
• Add a preview version of the de-novo pipeline

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.28.4-beta...v0.28.5-beta