added new screenshots

README.md

@@ -6,9 +6,9 @@ The CPSR workflow is integrated with the framework that underlies the [Personal
 
 *CPSR* accepts a query file from a single case/patient, containing raw germline variant calls encoded in the [VCF](https://samtools.github.io/hts-specs/VCFv4.2.pdf) format (i.e. SNVs/InDels). A comprehensive set of **virtual cancer predisposition gene panels** harvested from the [Genomics England PanelApp](https://panelapp.genomicsengland.co.uk/) allows the user to flexibly put a restriction on which genes and findings are displayed in the cancer predisposition report.
 
-Snapshots of sections in the cancer predisposition genome report:
+Snapshots of sections in the cancer predisposition genome report (artificial sample, with more findings than usual) are shown below:
 
-![CPSR views](pkgdown/assets/img/cpsr_views.png)
+![CPSR views](pkgdown/assets/img/cpsr_sc.png)
 
 ## News
 
@@ -40,7 +40,7 @@ Snapshots of sections in the cancer predisposition genome report:
 
 ## Example report
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6223386.svg)](https://doi.org/10.5281/zenodo.6223386)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11401491.svg)](https://doi.org/10.5281/zenodo.11401491)
 
 ## Getting started
 

pkgdown/index.md

@@ -18,7 +18,7 @@ The workflow is integrated with the framework that underlies [Personal Cancer Ge
 
 Snapshots of sections in the cancer predisposition genome report:
 
-![](img/cpsr_views.png)
+![](img/cpsr_sc.png)
 
 <br>
 
@@ -55,7 +55,7 @@ Snapshots of sections in the cancer predisposition genome report:
 
 ### Example report
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6223386.svg)](https://doi.org/10.5281/zenodo.6223386)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11401491.svg)](https://doi.org/10.5281/zenodo.11401491)
 
 ### Getting started
 

vignettes/CHANGELOG.Rmd

@@ -24,9 +24,9 @@ output: rmarkdown::html_document
   - Users need to download an assembly-specific VEP cache separately from PCGR/CPSR, and provide its path to the new required argument `--vep_dir` in the `cpsr` command
 - 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](https://rpubs.com/sigven/pcgr_refdata).
+  - 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, amenable e.g. for aggregation of results across samples
+- A multi-sheet Excel workbook output with variant classifications and biomarker findings are provided, suitable e.g. for aggregation of results across samples
 - 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)