1 changed files with 2 additions and 1 deletions
+ 2
- 1
tasks/bcftools.wdl
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| @@ -13,9 +13,10 @@ task bcftools { | |||
| if [ ${PONmode} ]; then | |||
| mkdir -p /cromwell_root/tmp/bcftools/ | |||
| cp ${pon_vcf}/*.vcf /cromwell_root/tmp/bcftools/ | |||
| #for i in ${sep=" " pon_vcf} | |||
| #do | |||
| for i in ${pon_vcf}/*.vcf | |||
| for i in /cromwell_root/tmp/bcftools/*.vcf | |||
| do | |||
| bcftools view $i -Oz -o /cromwell_root/tmp/bcftools/$i.gz | |||
| done | |||
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