From 651780e77bbdd7919f58333131e7597b789122ad Mon Sep 17 00:00:00 2001 From: Sigve Nakken Date: Wed, 26 Jun 2024 10:50:45 +0200 Subject: [PATCH] polish docs before release --- README.md | 2 +- pcgrr/vignettes/CHANGELOG.Rmd | 3 ++- pcgrr/vignettes/installation.Rmd | 4 ++++ 3 files changed, 7 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 40efaffb..4cd1d1ba 100755 --- a/README.md +++ b/README.md @@ -26,7 +26,7 @@ PCGR supports both of the most recent human genome assemblies (grch37/grch38), a ### News -- *June 2024*: **2.x.x release** +- *June 2024*: **2.0.0 release** - Massive reference data bundle upgrade, new report layout, oncogenicity classification++ - Details at [CHANGELOG](http://sigven.github.io/pcgr/articles/CHANGELOG.html) diff --git a/pcgrr/vignettes/CHANGELOG.Rmd b/pcgrr/vignettes/CHANGELOG.Rmd index 91dd9191..a593fb4a 100644 --- a/pcgrr/vignettes/CHANGELOG.Rmd +++ b/pcgrr/vignettes/CHANGELOG.Rmd @@ -48,7 +48,7 @@ pdiakumis <- user("pdiakumis") ## v2.0.0 -* Date: **2024-06-xx** +* Date: **2024-06-26** * Major data updates * ClinVar * NCI Thesaurus @@ -73,6 +73,7 @@ pdiakumis <- user("pdiakumis") - Re-engineered data bundle generation pipeline - Improved data bundle documentation - An HTML report with an overview of the contents of the data bundle is shipped with the reference data itself, also available [here (grch38)](https://rpubs.com/sigven/pcgr_refdata). +- Singularity/Apptainer support - Moved more of the code base to initial Python workflow steps (biomarker matching, CNA segment annotation, RNA expression analysis, oncogenicity classification) - Variants are now classified with respect to both oncogenicity and actionability, and the previous global tier classification (tier 1-5) is thus deprecated - New copy number input format - allele-specific (chrom, start, end, n_major, n_minor) diff --git a/pcgrr/vignettes/installation.Rmd b/pcgrr/vignettes/installation.Rmd index ef3864b8..05e8204d 100644 --- a/pcgrr/vignettes/installation.Rmd +++ b/pcgrr/vignettes/installation.Rmd @@ -255,3 +255,7 @@ apptainer exec \ --tumor_af_tag "TAF" \ --vcf2maf ``` + +If you run into issues or problems related to apptainer/singularity, we appreciate if you can try to +resolve them directly through the apptainer community. The authors of PCGR/CPSR have limited experience with apptainer, and we thus cannot offer extensive feedback on issues related to such matters. +