1 changed files with 3 additions and 3 deletions
+ 3
- 3
tasks/bamdst.wdl
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| @@ -11,9 +11,9 @@ task bamdst { | |||
| command <<< | |||
| set -o pipefail | |||
| set -e | |||
| mkdir -p /cromwell_root/tmp/bamdst | |||
| bamdst -p ${bed} -o /cromwell_root/tmp/bamdst ${bam} | |||
| cd /cromwell_root/tmp/bamdst | |||
| mkdir -p /cromwell_root/tmp/bamdst/ | |||
| /bamdst/bamdst -p ${bed} -o /cromwell_root/tmp/bamdst/ ${bam} | |||
| cd /cromwell_root/tmp/bamdst/ | |||
| cp chromosomes.report ${sample}_chromosomes.report | |||
| cp coverage.report ${sample}_coverage.report | |||
| cp depth_distribution.plot ${sample}_depth_distribution.plot | |||
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