pipeline-call-gSNP v10.1.0-rc.1

What's Changed

• Update description with standards by @yashpatel6 in #161
• Use GVCFs for genotyping - run time/CPU hours substantially reduced (0.52) by @sorelfitzgibbon in #158
• Bump external/pipeline-Nextflow-module from 9db08f0 to ef40c10 by @dependabot in #169
• Bump external/pipeline-Nextflow-config from 3ec7186 to be1eaf5 by @dependabot in #170

Full Changelog: v10.0.1...v10.1.0-rc.1

call-gSNP v10.0.1

What's Changed

• Add PlantUML flow diagram by @nwiltsie in #157
• Resolve intervals path by @yashpatel6 in #160

Full Changelog: v10.0.0...v10.0.1

call-gSNP v10.0.0

What's Changed

• Standardize filenames by @yashpatel6 in #122
• Enable input deletion for metapipeline by @yashpatel6 in #127
• Release 10.0.0-rc.1 by @yashpatel6 in #129
• Set default IR compression to 1 by @yashpatel6 in #131
• Save tumor segmentation file by @yashpatel6 in #130
• Emit all confident sites by @yashpatel6 in #110
• Pipeline update to only variant calling by @yashpatel6 in #136
• Validation and resource updater by @yashpatel6 in #137
• Resource allocation bugfix by @yashpatel6 in #138
• Autofix broken Confluence links by @nwiltsie in #139
• Enable dependabot to keep submodules up-to-date by @nwiltsie in #140
• Bump external/pipeline-Nextflow-config from c77aeca to 3ec7186 by @dependabot in #146
• Add standard pipeline GitHub workflows by @nwiltsie in #152
• Bump external/pipeline-Nextflow-module from 4bc4336 to 9db08f0 by @dependabot in #144
• Release 10.0.0 by @yashpatel6 in #154

New Contributors

• @nwiltsie made their first contribution in #139
• @dependabot made their first contribution in #146

Full Changelog: v9.2.1...v10.0.0

call-gSNP v10.0.0-rc.3

CHANGELOG

Added

• Validation with PipeVal
• Custom resource allocation updates through configuration parameters

call-gSNP v10.0.0-rc.2

CHANGELOG

Added

• Save tumor segmentation QC output from CalculateContamination

Changed

• Set default compression for GATK IndelRealignment to 1
• Make pipeline germline variant calling only

Removed

• BAM processing steps

call-gSNP v10.0.0-rc.1

CHANGELOG

Added

• Option to delete input data files for metapipeline disk usage optimization

Changed

• Standardize output file names

call-gSNP v9.2.1

CHANGELOG

Fixed

• Remove duplicated records based on only 11 required fields of each record

call-gSNP v9.2.0

CHANGELOG

Added

• F32.config for resource allocation

Changed

• Use external resource allocation module
• Parameterize Docker registry
• Use ghcr.io/uclahs-cds as default registry

call-gSNP v9.1.0

CHANGELOG

Added

• IndelRealignment compression parameter
• Param validation

Changed

• Parse CSV inputs using modularized csv_parser
• Delete merged but un-deduplicated BAMs earlier for more efficient disk usage

Fixed

• Bug with M64 and F2 detection

call-gSNP v9.0.1

CHANGELOG

Fixed

• Bug with improper output directory due to CSV parsing error