bed file format bug fix

broadinstitute · Jul 3, 2024 · adaa808 · adaa808
1 parent 7fa5bf9
commit adaa808
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/CNV-Profiler/CNV-Profiler.wdl b/CNV-Profiler/CNV-Profiler.wdl
@@ -131,7 +131,10 @@ task GetPaddedCnvBed {
 
         with open('padded_cnv.bed', 'a') as f:
             for interval in padded_cnv_interval_list:
-                f.write(interval + '\n')
+                chrom = interval.split(':')[0]
+                start = interval.split(':')[1].split('-')[0]
+                end = interval.split(':')[1].split('-')[1]
+                f.write("{chr}\t{start}\t{end}" + '\n')
         CODE
     >>>
     runtime {