first commit

tasks/bcftools.wdl

@@ -22,6 +22,7 @@ task bcftools {
 			bcftools view ${pon_vcf3} -Oz -o /cromwell_root/tmp/bcftools/$(basename $pon_vcf3).gz
 			
 			cd /cromwell_root/tmp/bcftools
+			ls
 			bcftools index *.vcf.gz
 
 			bcftools merge -m all -f PASS,. --force-samples *.vcf.gz |\