Skip to content

Latest commit

 

History

History
82 lines (66 loc) · 2.76 KB

CHANGELOG.md

File metadata and controls

82 lines (66 loc) · 2.76 KB

Changelog

All notable changes to the calculate-targeted-coverage pipeline.

The format is based on Keep a Changelog.

This project adheres to Semantic Versioning.

[Unreleased]

Changed

  • Update Nextflow configuration test workflows
  • Update README Performance Validation and References section
  • Remove unused docker image for bedr
  • Update metadata description to match repo description
  • Update documentation of utility script for joining per-sample outputs

[v1.1.0] - 2024-03-28

Added

  • Compressed output for the expanded set of target intervals

[v1.0.0] - 2024-03-27

Added

  • Add workflow to generate SVG images from embedded PlantUML source
  • Add workflow to build and deploy documentation to GitHub Pages
  • Add workflow to run Nextflow configuration regression tests
  • Add NFTest infrastructure and test cases
  • Add one Nextflow regression test
  • Add Plant UML diagram for pipeline workflow
  • Add parameter validation schema

Changed

  • Update CI/CD workflow to use current image
  • Update samtools depth default output options
  • Update filenames to standardized format

[v1.0.0-rc.2] - 2024-02-14

Changed

  • Update pipeline name to match Boutros Lab standards

[v1.0.0-rc.1] - 2024-01-09

Added

  • Add get_depth_samtools.nf module
  • Add merge_intervals_bedtools.nf module
  • Add depth_to_bed.nf module
  • Add preliminary configs
  • Add main workflow
  • Add run_HS_metrics.nf module
  • Add parameters for providing extra arguments to process tools
  • Add option to include target and bait bed files or interval target files
  • Add external script for joining single sample outputs
  • Add module process to generate interval list from bait bed
  • Add conditional logic to take target bed with bait bed and/or pre-built interval lists for targets and/or baits
  • Add workflow for calculating coverage at select off-target loci
  • Add workflow for creating a new interval file with target intervals merged with coverage-enriched off-target dbSNP sites.
  • Add flow diagram of pipeline steps.
  • Add checksum creation
  • Add resource allocation for all processes in all partition types
  • Add pipeline release github workflow

Changed

  • Update manifest
  • Update metadata.yaml
  • Update output directory structure according to lab standards
  • Update workflow to accept external bait file.
  • Update docker container registry to ghcr.io/uclahs-cds
  • Add coverage cap parameter to CollectHsMetrics command
  • Add default parameter definitions for coverage cap and external bait file
  • Update template.config for target bed +/- bait bed, bait interval list, or target interval list
  • Update default parameters.
  • Update methods.config to match current template and use external module.