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tasks/bedtools.wdl
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| command <<< | command <<< | ||||
| set -e -o pipefail | set -e -o pipefail | ||||
| mkdir -p /cromwell_root/tmp/bedtools | mkdir -p /cromwell_root/tmp/bedtools | ||||
| mv ${sep=' ' bam} /cromwell_root/tmp/bedtools | |||||
| cp ${sep=' ' bai} /cromwell_root/tmp/bedtools | |||||
| cd /cromwell_root/tmp/bedtools | cd /cromwell_root/tmp/bedtools | ||||
| bedtools multicov -bams ${sep=' ' bam} -bed ${bed_file} > revread_count.txt | bedtools multicov -bams ${sep=' ' bam} -bed ${bed_file} > revread_count.txt | ||||
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