first commit

tasks/bcftools.wdl

@@ -15,13 +15,6 @@ task bcftools {
 		
 		if [ ${PONmode} ]; then
 			mkdir -p /cromwell_root/tmp/bcftools/
-			#for i in ${sep=" " pon_vcf}
-			#do
-			#for i in ${pon_vcf}/*
-			#do 
-			#	cp $i /cromwell_root/tmp/bcftools/
-			#	bcftools view /cromwell_root/tmp/bcftools/$i -Oz -o /cromwell_root/tmp/bcftools/$i.gz
-			#done
 			
 			cp ${pon_vcf1} /cromwell_root/tmp/bcftools/
 			bcftools view /cromwell_root/tmp/bcftools/${pon_vcf1} -Oz -o /cromwell_root/tmp/bcftools/${pon_vcf1}.gz
@@ -29,7 +22,7 @@ task bcftools {
 			bcftools view /cromwell_root/tmp/bcftools/${pon_vcf2} -Oz -o /cromwell_root/tmp/bcftools/${pon_vcf2}.gz
 			cp ${pon_vcf3} /cromwell_root/tmp/bcftools/
 			bcftools view /cromwell_root/tmp/bcftools/${pon_vcf3} -Oz -o /cromwell_root/tmp/bcftools/${pon_vcf3}.gz
-			
+
 			bcftools merge -m any -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz |\ 
 			bcftools plugin fill-AN-AC |\ 
 			bcftools filter -i 'SUM(AC)>1' > panel_of_normal.vcf