polish docs for release

Author: sigven

README.md

@@ -12,16 +12,12 @@ Snapshots of sections in the [quarto](https://quarto.org)-based cancer predispos
 
 ## News
 
--   *June 2024*: **2.x.x release**
-    -   New HTML report generation and layout with [quarto](https://quarto.org/)
-    -   Excel output supported
-    -   Updated virtual gene panels (Genomics England PanelApp, Cancer Gene Census)
-    -   Reference data updates, most importantly including 
-        - ClinVar - June 2024
-        - CIViC - June 2024
-        - GENCODE - v46
-    -   Software updates - VEP 112
-    -   Extensive code clean-up and re-structuring
+-   *June 2024*: **2.0.0 release**
+    - New HTML report generation and layout with [quarto](https://quarto.org/)
+    - Excel output supported
+    - Data bundle update
+    - Singularity/Apptainer support
+    - [CHANGELOG](http://cpsr.readthedocs.io/en/latest/CHANGELOG.html)
 
 -   *November 2022*: **1.0.1 release**
     -   Added CPSR logo (designed by [Hal Nakken](https://halvetica.net))

pkgdown/index.md

@@ -24,16 +24,12 @@ Snapshots of sections in the [quarto](https://quarto.org)-based cancer predispos
 
 ### News
 
-* *June 2024*: **2.x.x release**
+* *June 2024*: **2.0.0 release**
   - New HTML report generation and layout with [quarto](https://quarto.org/)
   - Excel output supported
-  - Updated virtual gene panels (Genomics England PanelApp, Cancer Gene Census)
-  - Reference data updates, most importantly including 
-    - ClinVar - June 2024
-    - CIViC - June 2024
-    - GENCODE - v46
-  - Software updates - VEP 112
-  - Extensive code clean-up and re-structuring
+  - Data bundle update
+  - Singularity/Apptainer support
+  - [CHANGELOG](http://cpsr.readthedocs.io/en/latest/CHANGELOG.html)
 
 * *November 2022*: **1.0.1 release**
   * Added CPSR logo (designed by [Hal Nakken](https://halvetica.net))

vignettes/CHANGELOG.Rmd

@@ -5,7 +5,7 @@ output: rmarkdown::html_document
 
 ## v2.0.0
 
-* Date: **2024-06-xx**
+* Date: **2024-06-26**
 * Data updates
   * ClinVar
   * GWAS catalog
@@ -27,6 +27,7 @@ output: rmarkdown::html_document
   - 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).
 - Cleaned up code base for reporting and classification
 - A multi-sheet Excel workbook output with variant classifications and biomarker findings are provided, suitable e.g. for aggregation of results across samples
+- Singularity/Apptainer support
 - argument name changes to `cpsr`:
   - `--pcgr_dir` is now named `--refdata_dir`
   - `--clinvar_ignore_noncancer` is now named `--clinvar_report_noncancer`, meaning that variants found in ClinVar, yet attributed to _non-cancer related_ phenotypes, are now excluded from reporting by default)

vignettes/running.Rmd

@@ -193,7 +193,7 @@ usage:
 
 ## Example run
 
-The *cpsr* R package comes with a test VCF file (calls from the GRCh37 human genome assembly) that can be used to test the CPSR workflow. Please note that these are artificial germline calls, not originating form an actual patient.
+The *cpsr* R package comes with a test VCF file (calls from the GRCh37 human genome assembly) that can be used to test the CPSR workflow. Please note that these are artificial germline calls, not originating from an actual patient.
 
 Report generation with the example VCF, using the [Adult solid tumours cancer susceptibility](https://panelapp.genomicsengland.co.uk/panels/245/) as the virtual gene panel, can be performed through the following command: