v0.28.4-beta

Updates include

SV discovery algorithms:

• Update manta to 1.6.0
• Optimize Scramble

New functionality:

• Add PED file validation to GatherBatchEvidence and as standalone script

Documentation and CI/CD:

• Add Scramble docker to the build script & update docs
• Clarify single-batch vs. multi-batch workflows in cohort mode Terra workspace on dashboard

Updates and bug fixes:

• Remove redundant GetPed task in GatherBatchEvidence.CNMOPS
• Make genome_tracks optional in FilterGenotypes
• Toggle Collect PESR/Counts in GatherSampleEvidence with booleans
• Fix allosomes_list bug
• Filter mCNVs under 5kbp
• Remove hgdp_1kgp_ped test batch input from MainVcfQc template
• Fix melt insert size input type in EvidenceQC
• Correct use of optimize_vcf_records_per_shard in FilterGenotypes
• Update JoinRawCalls formatter arg in template
• Check for empty scatter in GenotypeDepthPart2
• Make the Cromwell root config in the MELT workflow portable

Full Changelog: v0.28.3-beta...v0.28.4-beta

v0.28.3-beta

Updates include

• Remove CHR2 and END2 for CPX at the end of CleanVcf
• Add TSV rename map option to RenameVcfSamples
• Add required index files to hg38 resources
• Add Docker images build instructions to the docs
• Add PlotSVCountsPerSample subworkflow to the end of ClusterBatch and FilterBatchSites

Full Changelog: v0.28.2-beta...v0.28.3-beta

v0.28.2-beta

Updates include

• Add high-level description of docker images and their build process
• Remove max GQ filtering from per sample QC
• Update protein-coding GTF to MANE v1.2
• Reference panel resources and critical bug fixes
• Add FilterGenotypes workflow
• Remove use of the file command
• Move PESR genotyping filter statuses to info fields
• Bug fix building samtools-cloud docker
• Bug fix Github actions out of disk error
• Sharded AnnotateVcf workflow
• Add Terra validation to Github actions
• Resolve new linting errors
• Deduplicate records and CPX variant IDs in ResolveComplexVariants

Full Changelog: v0.28.1-beta...v0.28.2-beta

v0.28.1-beta

This release incorporates the updated docker images from v0.28-beta.

Updates

• Fix a bug committing changes to dockers_*.json after an image is updated
• Delete some commented lines in drop_empty_records.py to prompt docker build

Full Changelog: v0.28-beta...v0.28.1-beta

v0.28-beta

Note: This version corresponding to v0.28-beta does not have updated docker images. The docker image updates are now reflected in v0.28.1-beta so that version should be used instead.

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: v0.27.3-beta...v0.28-beta

v0.27.3-beta

What's Changed

• Update README for docker build script
• Fix for tiny shard of IntegrateGQ in single sample pipeline
• Set minimum PE count of 1 during genotyping

Full Changelog: v0.27.2-beta...v0.27.3-beta

v0.27.2-beta

What's Changed

• Add missing space in functional annotation to enable optional settings
• Eliminate cram to bam conversion when possible
• Add ref panel inputs for MakeCohortVcf subworkflows
• Extend STR workflow to collect additional locus-level metrics
• Change ref allele to N if unsupported during vcf standardization
• Add sample renaming for SD files in GatherBatchEvidence
• Remove vcf header contig sorting in CleanVcf5
• Add support for building dockers for multiple registries
• Remove non-public images from the git-sha-based target determination in docker build script

Full Changelog: v0.27.1-beta...v0.27.2-beta

v0.27.1-beta

What's Changed

• Add handling for Flag vcf fields to vcf_to_pandas
• Add outlier samples list & count outputs to PlotSVCountsPerSample

Full Changelog: v0.27-beta...v0.27.1-beta

v0.27-beta

What's Changed

• New RdTest mode for very large variants
• Updates to the documentation website, its build action, and the Algolia configuration
• CleanVcfPart5 fix
• Add legacy file support for BatchEvidenceMerging

Full Changelog: v0.26.10-beta...v0.27-beta

v0.26.10-beta

Updates

• Update WDLs to adhere with implicit coercions requirement
• Update the style of build_docker.py
• Remove depth vcf from pesr merging in FilterBatchSamples
• Maintain a mirror of images on GCR and ACR
• Set target images for Azure based on commit SHA

Full Changelog: v0.26.9-beta...v0.26.10-beta