first commit

tasks/bcftools.wdl

@@ -19,7 +19,7 @@ task bcftools {
 			bcftools view ${pon_vcf2} -Oz -o /cromwell_root/tmp/bcftools/$(basename ${pon_vcf1}.gz)
 			bcftools view ${pon_vcf3} -Oz -o /cromwell_root/tmp/bcftools/$(basename ${pon_vcf1}.gz)
 			cd /cromwell_root/tmp/bcftools
-			for i in ${sep=" " *.vcf.gz}
+			for i in `ls *.gz`
 			do
 			bcftools index $i
 			done