1 changed files with 3 additions and 3 deletions
+ 3
- 3
tasks/bamdst.wdl
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| command <<< | command <<< | ||||
| set -o pipefail | set -o pipefail | ||||
| set -e | 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 chromosomes.report ${sample}_chromosomes.report | ||||
| cp coverage.report ${sample}_coverage.report | cp coverage.report ${sample}_coverage.report | ||||
| cp depth_distribution.plot ${sample}_depth_distribution.plot | cp depth_distribution.plot ${sample}_depth_distribution.plot |
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