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CHANGELOG.md

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Changelog

All notable changes to pipeline-Nextflow-module.

The format is based on Keep a Changelog.

This project adheres to Semantic Versioning.

[Unreleased]

Added

  • Add indexFile module to return index file path
  • Add intermediate file/directory removal module
  • Add genome interval extraction module
  • Add PipeVal validation module
  • Add index file module
  • Add standardized filename generation module
  • Add exposed string sanitization function
  • Add options to handle compressed files with VCF indexing workflow
  • Add bgzip to index_VCF_tabix module
  • Add PipeVal generate-checksum module
  • Add run_validate_PipeVal_with_metadata method

Changed

  • Use ghcr.io/uclahs-cds as default registry
  • Initial pipeline set up
  • Update log output directory for intermediate file removal
  • File deletion module: add disk usage monitoring before and after deletion
  • PipeVal module: nested log directories
  • Update PipeVal to v4.0.0-rc.2
  • Set ext.capture_logs to false for all processes to disable new setup_process_afterscript() behavior.
  • Change PipeVal command since the interface was changed.
  • Change indexFile to support cram format type