first commit

tasks/bcftools.wdl

@@ -18,18 +18,15 @@ task bcftools {
 			
 
 			bcftools view ${pon_vcf1} -Oz -o /cromwell_root/tmp/bcftools/$(basename $pon_vcf1).gz
-			bcftools index /cromwell_root/tmp/bcftools/$(basename $pon_vcf1).gz
-
 			bcftools view ${pon_vcf2} -Oz -o /cromwell_root/tmp/bcftools/$(basename $pon_vcf2).gz
-			bcftools index /cromwell_root/tmp/bcftools/$(basename $pon_vcf2).gz
-
 			bcftools view ${pon_vcf3} -Oz -o /cromwell_root/tmp/bcftools/$(basename $pon_vcf3).gz
-			bcftools index /cromwell_root/tmp/bcftools/$(basename $pon_vcf3).gz
+			
+			bcftools index /cromwell_root/tmp/bcftools/*.vcf.gz
 
 			bcftools merge -m all -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
-						
+
 		else
 			touch panel_of_normal.vcf
 		fi