v0.29-beta

What's Changed

Critical

This release includes a critical bug fix to the SplitVariants task in GenotypeBatch. The affected workflow was GenotypeBatch, and the affected version was v0.28.5-beta. We recommend immediately updating to v0.29-beta. If you ran GenotypeBatch with v0.28.5-beta, please check if any records were dropped. If in doubt, re-run with v0.29-beta. More details in #712

Pipeline functionality updates

• Integrate ReshardVcf into ResolveComplexVariants
• Remove CHR2 and END2 from INS in CleanVcf
• Fix --par arg to compute_AFs.py in ShardedAnnotateVcf
• Updates to allele frequency annotation fields
• Grouped MEIs with insertions in splitvariants.py

Performance improvements

• Reimplement ParseGenotypes in GenotypeComplexVariants
• Reduce memory usage in GenotypeSRPart1
• Set the default disk size in AnnotateIntervals as a function of input files size
• Making the Vapor plots optional to store as a final output
• Make per-sample QC plots optional in MainVcfQc

Fixing bugs and small annoyances

• Skip subsampling if batch size is less than n_samples_subsample
• Add NonZeroReferenceLengthAlignmentReadFilter read filter to CollectSVEvidence
• Prevent sample ID mangling in WGD computation
• Update gatk docker with changes to handle CPX_TYPE for CTX
• Fix UnboundLocalError in EvidenceQc
• Update gnomad-v2 sample-level benchmarking data path

Documentation

• Terra dashboard updates
• Reorganize docs on running the pipeline
• Add CONTRIBUTING.md
• Update Docusaurus and its dependencies to v3.3.2
• Update docs on building and hosting Docker images
• Update docs on building inputs
• Add documentation for rename_samples in GatherBatchEvidence

CI/CD, workflow organization, and auxiliary scripts

• Deprecate single-batch Terra configs
• Add support for incomplete workflows in get_inputs_outputs.py
• Trigger WDL tests on changes to /inputs and fix Terra config tests
• Update deprecated Pandas append operation for monitoring log analysis
• Extend the list supported syntax-highlighting languages

Full Changelog: v0.28.5-beta...v0.29-beta