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-bet