From 2ffebe2dc3d57665e651498c8a70f0d64688911a Mon Sep 17 00:00:00 2001 From: Sigve Nakken Date: Thu, 1 Aug 2024 15:10:01 +0200 Subject: [PATCH] update README and CHANGELOG --- README.md | 4 ++++ pcgrr/pkgdown/index.md | 5 ++++- pcgrr/vignettes/CHANGELOG.Rmd | 11 ++++++++++- 3 files changed, 18 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index a1e96135..3db33068 100755 --- a/README.md +++ b/README.md @@ -28,6 +28,10 @@ PCGR originates from the [Norwegian Cancer Genomics Consortium (NCGC)](http://ca ### Top News +- *August 1st 2024*: **2.0.3 release** + - patch to fix purity/ploidy propagation, MAF output for tumor-only runs, and other minor issues + - [CHANGELOG](http://sigven.github.io/pcgr/articles/CHANGELOG.html) + - *July 16th 2024*: **2.0.2 release** - patch to ensure correct reference to actionability guidelines - [CHANGELOG](http://sigven.github.io/pcgr/articles/CHANGELOG.html) diff --git a/pcgrr/pkgdown/index.md b/pcgrr/pkgdown/index.md index 408afc1a..9c9226c8 100644 --- a/pcgrr/pkgdown/index.md +++ b/pcgrr/pkgdown/index.md @@ -28,7 +28,10 @@ Example screenshots from the [quarto](https://quarto.org)-based cancer genome re PCGR originates from the [Norwegian Cancer Genomics Consortium (NCGC)](http://cancergenomics.no), at the [Institute for Cancer Research, Oslo University Hospital, Norway](http://radium.no). ### Top News - +- *August 1st 2024*: **2.0.3 release** + - patch to fix purity/ploidy propagation, MAF output for tumor-only runs, and other minor issues + - [CHANGELOG](http://sigven.github.io/pcgr/articles/CHANGELOG.html) + - *July 16th 2024*: **2.0.2 release** - patch to ensure correct reference to actionability guidelines - [CHANGELOG](http://sigven.github.io/pcgr/articles/CHANGELOG.html) diff --git a/pcgrr/vignettes/CHANGELOG.Rmd b/pcgrr/vignettes/CHANGELOG.Rmd index e8cb5739..2ce8dd76 100644 --- a/pcgrr/vignettes/CHANGELOG.Rmd +++ b/pcgrr/vignettes/CHANGELOG.Rmd @@ -46,10 +46,19 @@ sigven <- user("sigven") pdiakumis <- user("pdiakumis") ``` +## v2.0.3 + +- Date: **2024-08-01** +- Ensure correct propagation of purity/ploidy in output report +- Ensure that MAF output is properly filtered for tumor-only runs +- Ensure properly copying of quarto templates (abandon `file.copy`), +both for PCGR and CPSR + + ## v2.0.2 - Date: **2024-07-16** -- Ensure correct reference to variant actionability guidelines - AMP/ASCO/CAP (*not* ACMG/AMP), both in code and in docs (thanks to [HomoPolyethylen] for pointing this out) +- Ensure correct reference to variant actionability guidelines - AMP/ASCO/CAP (*not* ACMG/AMP), both in code and in docs (thanks to [HomoPolyethylen](https://github.com/HomoPolyethylen) for pointing this out) - fix bug in missing assignment of tier 3 variants (AMP/ASCO/CAP) - ensure non-exonic biomarker variants (e.g. TERT) are written to Excel sheet - specify (value boxes, plots) that MSI classification is based on coding variants