NEWS.md

gpgr 2.1.1

• 🐛 updating gene panel, fixes to pass devtools checks and pkgdown (pr82)

gpgr 2.1.0

• 🐛 minor fixes for canrep (pr81).

gpgr 2.0.0

• ⭐ add DRAGEN HRD in canrep (issue71 and pr72).
• ⭐ add BCFtools stats QUAL plot for somatic small variants ((issue70, pr73).
• 🔧 remove LINX support (pr74).
• ⭐ switch from Umccrise to sash inputs for canrep (pr68).

gpgr 1.5.0

• add bpi status in canrep summary table
• 🐛 LINX >= 1.23 has renamed codingContext to codingType in the breakend table (issue59, pr60).
  • also updated relevant DVC file
• 🐛 LINX >= 1.24 has added a reportableReasons in the fusion table (issue64, pr65).
• 🐛 pkgdown config needs to have .yml, not .yaml suffix (see r-lib/pkgdown#2244) (ci040bd2f).
• ⭐ build conda pkg for R v4.2 (ci0dbe49d).
• 🐛 LINX vis_copy_number tables that were empty were triggering mixedrank with an empty input (issue66, pr67).
  • ⭐ added row counts to tabs in LINX report in same PR.
• 🔧 use micromamba GitHub Action

gpgr 1.4.0

• 🐛 Update LINX cluster plot path pattern (issue50, pr51).
• ⭐ umccrise canrep: add SNV summary (pr53).
  • add hypermutated status in canrep summary table
• 🐛 Handle empty BPI Start/End values (pr55, issue54, umccrise issue88).
• 🐛 {gt} v0.7.0 requires a unique id for each tab_spanner (issue57, pr58).

gpgr 1.3.0 (2022-06-10)

• ⭐ Add Docker support (pr49).
• ⭐ Add conda-lock support (pr49).
• 🐛 Fix cancer report bugs (pr48).
• ⭐ Added CLI support for umccrise cancer report.
  • Modularised CLI subparsers into separate files
• 🔧 Refactored cancer report to use {sigrap} pkg for signature tools.
• 🔧 factorise ClusterId in LINX VisSvData table (pr46).
• 🔧 subset multiqc columns (commit-b7331db).

gpgr 1.2.0 (2022-02-07)

• ⭐ Support for DVC (pr43, issue41).
• 🔧 Fixes for LINX tables (pr40).
• 🔧 Bug fix for LINX CLI (8e89ac6).

gpgr 1.1.0 (2022-01-12)

• ⭐ Add LINX RMarkdown report.
• ⭐ Added script for tidying umccrised MultiQC JSON output (pr38).
• ⭐ Add CLI for LINX reporter (pr39).
• 🔧 Add LINX description tibble and refactor LINX code (pr36).

gpgr 1.0.0 (2021-12-22)

• Major change: Moving signature tool wrappers (CHORD, HRDetect, and MutationalPatterns) to sigrap (https://github.com/umccr/sigrap) (pr35).
• Support for LINX tables (pr34).

gpgr 0.2.0 (2021-11-23)

• new release after a year in the freezer
• ⭐ add CLI for CHORD, HRDetect and MutationalPatterns (pr26, pr28, issue17)
• ⭐ add 6 new SBS signatures from the March 2021 COSMIC release (v3.2) (issue22, pr23)
• ⭐ update to use the base pipe operator (|>) introduced in R 4.1 (pr24)
• ⭐ add handy get_genome_obj function that returns a BSgenome object, provided a 'hgXX' string (useful for MutationalPatterns & CHORD) (pr20)
• ⭐ add handy pkg_exists function that checks if the specified R package exists on the local system (pr20)
• ❓ add readr::local_edition(1) before readr::read_tsv due to readr using vroom under the hood (I'm not too comfortable with this, but anyway). See https://www.tidyverse.org/blog/2021/07/readr-2-0-0/#readr-2nd-edition. I think it happens because I'm using the comment parameter to read in the gzipped VCF. Oh well (pr21)
• 🔧 use bumpversion for updating pkg versions (issue18, pr19)
• 🔧 add pre-commit hooks and styler (issue25, pr27)

gpgr 0.1.0 (2020-11-19)

• Handle umccrise cancer report functionality:
  • PURPLE CNVs
  • SVs (tables + BND plots)
  • AF (summary + plot)
  • HRD
  • write final tables to tsv + json
  • Support for MutationalPatterns v3.0 (https://github.com/UMCUGenetics/MutationalPatterns)
  • Support for PURPLE v2.51+

gpgr 0.0.6 (2020-10-09)

• Initial release of gpgr. Features include:
  • Support for CHORD (https://github.com/UMCUGenetics/CHORD)
  • Support for HRDetect (https://github.com/Nik-Zainal-Group/signature.tools.lib)
  • Support for PURPLE (https://github.com/hartwigmedical/hmftools/tree/master/purple)
  • R package webpage deployed via GitHub Actions at https://umccr.github.io/gpgr/