first commit

tasks/bcftools.wdl

@@ -13,9 +13,10 @@ task bcftools {
 		
 		if [ ${PONmode} ]; then
 			mkdir -p /cromwell_root/tmp/bcftools/
+			cp ${pon_vcf}/*.vcf /cromwell_root/tmp/bcftools/
 			#for i in ${sep=" " pon_vcf}
 			#do
-			for i in ${pon_vcf}/*.vcf
+			for i in /cromwell_root/tmp/bcftools/*.vcf
 			do 
 				bcftools view $i -Oz -o /cromwell_root/tmp/bcftools/$i.gz
 			done