1 changed files with 1 additions and 3 deletions
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tasks/samtools.wdl
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| command <<< | command <<< | ||||
| set -o pipefail | set -o pipefail | ||||
| set -e | |||||
| set -e | |||||
| mkdir -p /cromwell_root/tmp/ | mkdir -p /cromwell_root/tmp/ | ||||
| cp ${bam_file} /cromwell_root/tmp/ | cp ${bam_file} /cromwell_root/tmp/ | ||||
| /opt/conda/bin/samtools index -b /cromwell_root/tmp/${bam_id} | /opt/conda/bin/samtools index -b /cromwell_root/tmp/${bam_id} |
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