first commit

tasks/bcftools.wdl

@@ -17,11 +17,11 @@ task bcftools {
 			mkdir -p /cromwell_root/tmp/bcftools/
 			
 
-			bcftools view ${pon_vcf1} -Oz -o /cromwell_root/tmp/bcftools
+			bcftools view ${pon_vcf1} -Oz -o /cromwell_root/tmp/bcftools/$(basename $pon_vcf1).gz
 
-			bcftools view ${pon_vcf2} -Oz -o /cromwell_root/tmp/bcftools
+			bcftools view ${pon_vcf2} -Oz -o /cromwell_root/tmp/bcftools/$(basename $pon_vcf2).gz
 
-			bcftools view ${pon_vcf3} -Oz -o /cromwell_root/tmp/bcftools
+			bcftools view ${pon_vcf3} -Oz -o /cromwell_root/tmp/bcftools/$(basename $pon_vcf3).gz
 
 			bcftools merge -m any -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz |\ 
 			bcftools plugin fill-AN-AC |\