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Changelog

All notable changes to the pipeline-recalibrate-BAM pipeline.

The format is based on Keep a Changelog.

This project adheres to Semantic Versioning.

[Unreleased]

[Changed]

  • Update Nextflow configuration test workflows

[1.0.0] - 2024-03-13

[Added]

  • Sort BAMs before merging for consistent order of output BAM @PG header lines
  • Add NFTest case
  • Add new flow diagram to README
  • Add additional details to Pipeline Steps section of README
  • Option to provide base recalibration tables for any subset of samples to skip BaseRecalibrator
  • Output pipeline parameters to log directory using store_object_as_json
  • Add Action to deploy documentation to GitHub Pages
  • Add Nextflow configuration test action and two regression tests
  • Add requirements to README

[Changed]

  • Use modularized set_env function
  • Use modularized check_limits function

[1.0.0-rc.4] - 2023-09-29

[Fixed]

  • Resource updater to allow update for all processes
  • Channel handling to save contamintion estimate files

[1.0.0-rc.3] - 2023-08-09

[Added]

  • Customization options for which input BAMs to delete with metapipeline

[1.0.0-rc.2] - 2023-08-02

[Added]

  • Custom resource allocation updates through configuration parameters

[1.0.0-rc.1] - 2023-07-27

[Added]

  • Basic configuration setup
  • Input YAML templates and handling
  • Per-patient input YAML handling
  • Interval splitting process, either per-chromosome by default or scattered
  • Indel Realignment workflow
  • BQSR workflow
  • Merging workflow
  • Contamination and depth of coverage processes
  • Input deletion
  • Intermediate file deletion
  • Schema validation
  • Documentation