output

codescripts/filter_indel_over_50_mendelian.py

@@ -1,4 +1,5 @@
 from itertools import islice
+import fileinput
 import sys, argparse, os
 
 
@@ -35,8 +36,8 @@ def process(line):
 	else:
 		outfile.write(line)
 
-input_file = open(input_dat)
-for line in fileinput.input(input_file):
+
+for line in fileinput.input(input_dat):
 	process(line)
 
 

tasks/merge.wdl

@@ -34,6 +34,7 @@ task merge {
 	output {
 		File family_all_info = "${family_name}.mendelian.txt"
 		File snv = "${family_name}.mendelian.snv.txt"
+		File indel_raw = "${family_name}.mendelian.indel.txt"
 		File indel = "${family_name}.mendelian.indel.lessthan50bp.txt"
 		File family_snv = "${family_name}.mendelian.snv.summary.txt"
 		File family_indel = "${family_name}.mendelian.indel.summary.txt"