polish docs before release

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)
 

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)

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.
+