v1.1.1

What's Changed

• Update cluster reference paths by @nwiltsie in #31
• Require user-provided Funcotator data source by @nkwang24 in #30

Full Changelog: v1.1.0...v1.1.1

v1.1.0

What's Changed

Added

• Add Delly2-sSV support
• Add preprocessing script for Strelka2 VCFs to add GT field for Funcotator
• Add process to split large VCFs to parse in chunks

Changed

• Standardize annotation workflow to always annotate variants after LiftOver
• Rename Delly2 to Delly2-gSV
• Upgrade to score version 1.20

Full Changelog: v1.0.0...v1.1.0

v1.0.0

What's Changed

• Simplify input parameters by @nwiltsie in #23
• Downgrade score, add proper verification tests by @nwiltsie in #24
• Fix unexpected factor renaming in SV branch by @nkwang24 in #27
• Update README by @nkwang24 in #25

Full Changelog: v1.0.0-rc.1...v1.0.0

v1.0.0-rc.1

What's Changed

• Bump the pipeline-submodules group with 2 updates by @dependabot in #1
• Bump external/pipeline-Nextflow-module from 537da32 to 1cfa9fa in the pipeline-submodules group by @dependabot in #5
• Bootstrap repository with minimal working pipeline by @nwiltsie in #4
• Rearrange processes and modules, add SV workflow for Delly2 by @nwiltsie in #8
• Update GATK version by @nkwang24 in #12
• Add method description to README by @nkwang24 in #11
• Add support for GRCh38->GRCh37 by @nwiltsie in #15
• Update Rscripts by @nkwang24 in #20

New Contributors

• @dependabot made their first contribution in #1
• @nwiltsie made their first contribution in #4
• @nkwang24 made their first contribution in #12

Full Changelog: https://github.com/uclahs-cds/pipeline-StableLift/commits/v1.0.0-rc.1