1 changed files with 3 additions and 2 deletions
+ 3
- 2
tasks/bedtools.wdl
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| @@ -10,8 +10,9 @@ task bedtools { | |||
| command <<< | |||
| set -e -o pipefail | |||
| path=$(dirname ${sep=' ' bam}) | |||
| mv ${sep=' ' bai} $path | |||
| mkdir -p /cromwell_root/tmp/bedtools | |||
| mv ${sep=' ' bam} /cromwell_root/tmp/bedtools | |||
| cd /cromwell_root/tmp/bedtools | |||
| bedtools multicov -bams ${sep=' ' bam} -bed ${bed_file} > revread_count.txt | |||
| >>> | |||
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