broadinstitute/gatk-sv: v0.28-beta

What's changed

Improvements to SR genotyping and INS breakpoints:

• Update SR counting and genotyping

Filtering workflows:

• Update ApplyManualVariantFilter json template
• Update VaPoR workflows
• SVConcordance workflows update
• Fix CTX END2 error in GATK formatting script

Other workflows:

• Fix non-deterministic errors in GetSampleIdsFromVcfTar
• make the RunMELT task a little more robust
• Improve STR workflow
• Remove DeleteIntermediateFiles task
• Remove unused ped_file input from GenotypeBatch and RegenotypeCNVs

Docker build:

• Manually install MASS R package in sv-pipeline-virtual-env
• Build and publish images to multiple registries in one job, & update the dependencies of the action

Other scripts, docs, and JSONs:

• Update copy_outputs.py
• Generate Terra workspace tsv files from transposed tables
• Update README to link to SV callers used
• Remove ped file from workspace data TSV for cohort mode terra workspace

Full Changelog: https://github.com/broadinstitute/gatk-sv/compare/v0.27.3-beta...v0.28-beta