fixed issues with sample names

Author: niekwit

workflow/scripts/peak_annotation_plots.R

@@ -18,8 +18,8 @@ txdb <- makeTxDbFromGFF(gtf)
 
 # Add sample names to bed files
 # Check which bed files are provided
-if (any(grepl("\\.overlap.bed$", bed.files)) == TRUE) {
-  samples <- sub(".*\\/([^\\/]+)\\.overlap.bed", "\\1", bed.files)
+if (any(grepl("\\.filtered.bed$", bed.files)) == TRUE) {
+  samples <- sub(".*\\/([^\\/]+)\\.filtered.bed", "\\1", bed.files)
 } else if (any(grepl("\\.overlap.filtered.bed$", bed.files)) == TRUE) {
   samples <- sub(".*\\/([^\\/]+)\\.overlap.filtered.bed", "\\1", bed.files)
 } else if (any(grepl("\\.narrowPeak$", bed.files)) == TRUE) {