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tasks/bcftools.wdl
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| if [ ${PONmode} ]; then | if [ ${PONmode} ]; then | ||||
| mkdir -p /cromwell_root/tmp/bcftools/ | mkdir -p /cromwell_root/tmp/bcftools/ | ||||
| cp ${pon_vcf}/*.vcf /cromwell_root/tmp/bcftools/ | |||||
| #for i in ${sep=" " pon_vcf} | #for i in ${sep=" " pon_vcf} | ||||
| #do | #do | ||||
| for i in ${pon_vcf}/*.vcf | |||||
| for i in /cromwell_root/tmp/bcftools/*.vcf | |||||
| do | do | ||||
| bcftools view $i -Oz -o /cromwell_root/tmp/bcftools/$i.gz | bcftools view $i -Oz -o /cromwell_root/tmp/bcftools/$i.gz | ||||
| done | done |
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