v0.16.0

Complete refactor of the dracarys R6 class system.

What's Changed

• docker: use multi-stage build by @pdiakumis in #122
• Support BCL Convert 4.2.7 by @pdiakumis in #124
• umccrise: refactor cancer report table parsers by @pdiakumis in #125
• Umccrise tidy by @pdiakumis in #127
• Sash support by @pdiakumis in #129
• TSO500 ctDNA v1 refactor by @pdiakumis in #133
• TSO500 ctDNA v2 support by @pdiakumis in #135
• MultiQC: add sash support by @pdiakumis in #137
• Use bump-my-version by @pdiakumis in #139
• NEWS v0.16.0 by @pdiakumis in #140

Full Changelog: v0.15.0...v0.16.0

v0.12.0

Mostly better handling of DRAGEN outputs, including FastQC metrics.

What's Changed

• umccrise: support presigned URL parsing by @pdiakumis in #94
• umccrise: support S3 outputs by @pdiakumis in #95
• multiqc: include more metrics in map by @pdiakumis in #98
• Oncoanalyser/sash/wts-qc/star-align metadata parsing by @pdiakumis in #101
• Major DRAGEN module refactor by @pdiakumis in #103
• Alignment QC reporter by @pdiakumis in #105
• Update GitHub Actions by @pdiakumis in #106

Full Changelog: v0.11.0...v0.12.0

Release 0.7.0

Summary

• Full Changelog: v0.6.0...v0.7.0

Mostly added use cases based on requests from the curation team related to
umccrise (CHORD, HRDetect, QC summary), PCGR, and MultiQC.

Deployments

• 🐳 Docker Image: v0.7.0
• 🐍 Conda package: v0.7.0

Details

• ⭐ Additions:

  • R functions:
    • umccr_tidy: workhorse that handles the tidying and method dispatch.
    • gds_file_presignedurl
  • R6 classes:
    • PcgrJsonFile
    • PcgrTiersFile
    • UmChordTsvFile
    • UmHrdetectTsvFile
    • UmQcSumFile
    • UmSigsSnvFile
    • MultiqcFile

• 🔧 Fixes:

  • Updated README with unified dracarys tidy CLI.
  • Added a fun column to FILE_REGEX for handling method dispatch.
  • GH Actions: Remove linux/arm64 from docker since conda pkgs don't generally have ARM64 equivalents.
  • GH Actions: use "miniforge-variant: Mambaforge"
    (see this issue).

• 🌴 Pull Requests Merged:

  • PCGR support by @pdiakumis in #23
  • Umccrise sigs/hrd support by @pdiakumis in #25