Skip to content

Latest commit

 

History

History
185 lines (144 loc) · 4.76 KB

CHANGELOG.md

File metadata and controls

185 lines (144 loc) · 4.76 KB
Raw

Changelog

All notable changes to the pipeline-call-gSNP pipeline.

The format is based on Keep a Changelog.

This project adheres to Semantic Versioning.

[Unreleased]

Added

  • NFTest test case

[10.1.0-rc.1]

Added

  • Add workflow for genotyping from GVCFs

Changed

  • Standardize description
  • Update GATK to 4.5.0.0

[10.0.1] - 2024-04-15

Changed

  • Replace workflow diagram with PlantUML version
  • Update PlantUML action to v1.0.1

Fixed

  • Resolve intervals before splitting to allow for index discovery

[10.0.0] - 2024-03-08

Added

  • Add workflow to generate SVG images from PlantUML
  • Add workflow to build and push documentation to GitHub Pages
  • Add workflow to run Nextflow configuration regression tests
  • Add CODEOWNERS file

Changed

  • Resource updater to allow update for all processes

Removed

  • Local resource-related function definitions

[10.0.0-rc.3] - 2023-08-16

Added

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

[10.0.0-rc.2] - 2023-07-25

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

[10.0.0-rc.1] - 2023-05-01

Added

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

Changed

  • Standardize output file names

[9.2.1] - 2023-01-25

Fixed

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

[9.2.0] - 2022-11-18

Added

  • F32.config for resource allocation

Changed

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

Added

  • Option to emit all confident sites in GVCFs

[9.1.0] - 2022-07-12

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

[9.0.1] - 2022-06-02

Fixed

  • Bug with improper output directory due to CSV parsing error

[9.0.0] - 2022-05-12

Added

  • Option for YAML input
  • Record deduplication workflow
  • Config for F16 node

Changed

  • Reorganize repo with pipeline entrypoint at root of repo and singular directory names

Fixed

  • Bug with records being duplicated through the parallelized processing of BAMs (#79)

[8.0.0] - 2022-03-14

Added

  • BETA: Support for paired inputs with a single normal sample and multiple tumour samples

Changed

  • Switch to SAMtools for indexing BAMs
  • Use sample ID and intervals as identifiers for log output directories
  • Standardize config structure
  • Partially revert BQSR parallelization and group ApplyBQSR by interval
  • Parallelize BaseRecalibrator per sample
  • Save VQSR output for QC
  • Save SNP+INDEL VQSRed VCF to output

[7.2.1] - 2022-01-25

Changed

  • Parallelize BQSR
  • Update .gitignore

Security

[7.2.0] - 2021-12-17

Changed

[7.1.0] - 2021-11-09

Added

  • Parallelize IR and BQSR in WXS/WES mode

Fixed

  • Fix targeted, single sample mode bugs

[7.0.0] - 2021-10-27

Added

  • Update call-gSNP to DSL2
  • Add GPL2 license
  • Parallelize MergeVcfs
  • Parallelize MergeSamFiles
  • Standardize output and log directories
  • Add process to remove intermediate files when save_intermediate_files is disabled
  • Parallelize GetPileupSummaries, CalculateContamination, and DepthOfCoverage processes
  • Split HaplotypeCaller process into process for VCF and GVCF modes
  • Parallelize GVCF HC process
  • Extract genome intervals from reference dictionary

Changed

  • Adjust static resource allocation to be more efficient
  • Auto-detect reference fasta dictionary
  • Rename ".bai" output files to ".bam.bai"
  • Auto-detect when in targeted mode and when in WGS mode