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CHANGELOG.md

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Changelog

All notable changes to the pipeline-name pipeline.

The format is based on Keep a Changelog.

This project adheres to Semantic Versioning.

[Unreleased]

Added

  • Add mosdepth quantize workflow
  • Add mosdepth coverage windows workflow
  • Add FastQC workflow
  • Add per readgroup and per library functionality
  • Add process_afterscript
  • Add Nextflow version requirement to README

Changed

  • Change to more descriptive algorithm names
  • Fixed CollectWgsMetrics params equal to zero bug
  • Update SAMtools 1.18 to 1.20
  • Update NFTest for FastQC and new test sample
  • Update repository/pipeline description
  • Update Nextflow configuration test workflows

[1.0.0] - 2024-03-12

Changed

  • Standardized input structure

[1.0.0-rc.1] - 2024-03-08

Added

  • Add schema.yaml
  • Add template.config
  • Add Qualimap bamqc
  • Add CollectWgsMetrics
  • Add F4.config
  • Add NFTest
  • Add SAMtools stats process
  • Add CODEOWNERS
  • Add example input YAMLs
  • Add pipeline-Nexflow-config as submodule
  • Add pipeline-Nextflow-module as submodule
  • Add workflow to build and deploy documentation GitHub Pages
  • Add workflow to run Nextflow configuration regression tests

Changed

  • Changed pipeline name pipeline-SQC-DNA to pipeline-generate-SQC-BAM
  • Use defaults for CollectWgsMetrics parameters
  • Pipeline name in output dir changed to generate-SQC-BAM
  • Changed remove_duplicates option to samtools_remove_duplicates
  • Update flow chart in README
  • Update README template
  • Update PR template
  • Use external indexFile function
  • Allow multiple BAM input
  • Input read_length through YAML
  • Use sanitize_uclahs_cds_id from pipeline-Nextflow-config
  • Update SAMtools 1.16.1 -> 1.18