1 changed files with 2 additions and 3 deletions
+ 2
- 3
tasks/bedtools.wdl
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| command <<< | command <<< | ||||
| set -e -o pipefail | set -e -o pipefail | ||||
| mkdir -p /cromwell_root/tmp/bedtools | |||||
| cp ${sep=' ' bai} /cromwell_root/tmp/bedtools | |||||
| cd /cromwell_root/tmp/bedtools | |||||
| path=$(dirname ${bam}) | |||||
| mv ${sep=' ' bai} $path | |||||
| 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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