Fix Rscript naming

analyses/copy_number_consensus_call/scripts/bed_to_segfile.R

@@ -131,7 +131,7 @@ cnvs <- cnvs %>%
 # read in the neutral regions
 neutral <- readr::read_tsv(
   opts$neutral_file, 
-  col_names = c("chrom", "start", "end", "specimen")
+  col_names = c("chrom", "start", "end", "Biospecimen")
 )
 
 # read in uncalled specimens
@@ -141,15 +141,15 @@ uncalled <- readr::read_tsv(opts$uncalled_file)
 # as these can not have any CN calls by definition, so we don't want to 
 # call them as unchanged, just missing (they won't appear in the cnv file)
 exclude_list <- uncalled %>% 
-  dplyr::group_by(sample)%>%
+  dplyr::group_by(Biospecimen)%>%
   dplyr::tally() %>%
   dplyr::filter(n > 1) %>%
-  dplyr::pull(sample)
+  dplyr::pull(Biospecimen)
 
 # filter out excluded samples from the neutral data and rearrange
 out_neutral <- neutral %>%
-  dplyr::filter(!(specimen %in% exclude_list)) %>%
-  dplyr::select(ID = specimen,
+  dplyr::filter(!(Biospecimen %in% exclude_list)) %>%
+  dplyr::select(ID = Biospecimen,
                 chrom = chrom,
                 loc.start = start, 
                 loc.end = end) %>%