first commit

tasks/bcftools.wdl

@@ -16,12 +16,12 @@ task bcftools {
 		if [ ${PONmode} ]; then
 			mkdir -p /cromwell_root/tmp/bcftools/
 			
-			cp ${pon_vcf1} /cromwell_root/tmp/bcftools/
-			bcftools view /cromwell_root/tmp/bcftools/${pon_vcf1} -Oz -o /cromwell_root/tmp/bcftools/${pon_vcf1}.gz
-			cp ${pon_vcf2} /cromwell_root/tmp/bcftools/
-			bcftools view /cromwell_root/tmp/bcftools/${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 view ${pon_vcf1} -Oz -o /cromwell_root/tmp/bcftools/${pon_vcf1}.gz
+
+			bcftools view ${pon_vcf2} -Oz -o /cromwell_root/tmp/bcftools/${pon_vcf2}.gz
+
+			bcftools view ${pon_vcf3} -Oz -o /cromwell_root/tmp/bcftools/${pon_vcf3}.gz
 
 			bcftools merge -m any -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz |\ 
 			bcftools plugin fill-AN-AC |\