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Changelog

Source: NEWS.md

gpgr 2.2.1

  • 🔧 make DRAGEN HRD parameter optional (pr94)
    • dragen_hrd parameter in cancer_rmd() function now defaults to NULL
    • CLI --dragen_hrd argument is no longer required
    • Report handles missing DRAGEN HRD data by showing “Missing” in HRD summary
    • Added warning message when no DRAGEN HRD file is supplied via CLI

gpgr 2.2.0

  • 📦 add support for PURPLE 4.2 output files (pr92)
    • Added gcContent column support in purple_cnv_som_gene_read() function for {tumor_name}.purple.cnv.gene.tsv files
    • Added TincLevel and ChimerismPercentage columns support in purple_qc_read() function for {tumor_name}.purple.qc.tsv files

gpgr 2.1.3

  • 🔧 adapt to eSVee SV format from oncoanalyser v2, temporarily disable CHORD (pr88)
    • Replace GRIDSS-specific SR/PR metrics with eSVee VF/DF/SF metrics
    • Remove SR and PR plots, update to use SF/DF plots for breakends
    • Update SV processing to handle eSVee format with new breakpoint matching logic
    • Temporarily disable CHORD functionality due to compatibility issues with eSVee calls
    • Remove MSI fields from cancer report summary table - always 0 since PURPLE 4.1 (sash#7)
    • Adapt Breakend ID assignment and mate matching in SV Map table with eSVee (issue89)
  • 🔧 filter PoN SV in cancer report tables (sash#8)

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)

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:

gpgr 0.0.6 (2020-10-09)