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} |