sample reports need to be neutered of TCGA-specificity: this can be done on CPTAC branch, at first
lib/GDCSampleReport.R should take "program" argument, populated by program value in config state of gdc_report.py when it launches the R script
consider making blacklist and reference directory optional args to R code: because the reference files are now installed to Python package (per #70) and blacklisting should be supported but not required
other links within .R file 9 (e.g. FFPE definition, etc) need to be updated to point to GDC, if necessary
other updates, as warranted by inspection of R code
noblem
commented
5 years ago
sample reports need to be neutered of TCGA-specificity: this can be done on CPTAC branch, at first