first commit

tasks/bcftools.wdl

@@ -22,9 +22,9 @@ task bcftools {
 			bcftools view ${pon_vcf3} -Oz -o /cromwell_root/tmp/bcftools/$(basename ${pon_vcf1}.gz)
 			
 			cd /cromwell_root/tmp/bcftools
-			bcftools index FUSCCTNBC083_pon.vcf.gz
-			bcftools index FUSCCTNBC330_pon.vcf.gz
-			bcftools index FUSCCTNBC467_pon.vcf.gz
+			bcftools index *.vcf.gz
+			#bcftools index FUSCCTNBC330_pon.vcf.gz
+			#bcftools index FUSCCTNBC467_pon.vcf.gz
 
 			bcftools merge -m all -f PASS,. --force-samples *.vcf.gz |\ 
 			bcftools plugin fill-AN-AC |\