Changelog • gpgr

gpgr 2.3.0

🔧 support for reading sigrap plots and data as inputs (input-sigrap-data branch)
- Add support for pre-generated sigrap mutational signature plots via PNG inputs
- Add new dependencies: png and grid packages for handling pre-generated plots
- Refactor mutational signatures section to support both live generation and pre-computed inputs
- Enable conditional logic to read from sigrap output directory when available
- Clarify CHORD/CHORD2 handling: CHORD outputs can now be provided as pre-computed input files (or produced via {sigrap}); gpgr will read and include CHORD results when available rather than attempting incompatible live computation. See PR #91 for details.
🐛 read is_hypermutated directly from bolt variant counts JSON instead of indirect proxy

🐛 restore hypermutated cancer report logic for current released sash/Bolt behavior.
- revert the premature switch to annotated > 500000
- restore inference from divergence between sage and annotated SNV counts

🔧 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

📦 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

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

🐛 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).

⭐ 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).

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

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)