first commit

tasks/bcftools.wdl

@@ -15,8 +15,10 @@ task bcftools {
 			mkdir -p /cromwell_root/tmp/bcftools/
 			#for i in ${sep=" " pon_vcf}
 			#do
-			bcftools view ${pon_vcf}/*.vcf -Oz -o /cromwell_root/tmp/bcftools/*.vcf.gz
-			#done
+			for i in ${pon_vcf}/*.vcf
+			do 
+				bcftools view $i -Oz -o /cromwell_root/tmp/bcftools/$i.gz
+			done
 			
 			bcftools merge -m any -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz |\ 
 			bcftools plugin fill-AN-AC |\