linzipeng
6 years ago
1 changed files with 2 additions and 2 deletions
+ 2
- 2
tasks/Dedup.wdl
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| command <<< | command <<< | ||||
| set -o pipefail | set -o pipefail | ||||
| set -e | set -e | ||||
| mv ${unsorted_bam} ./ | |||||
| /src/Bismark-0.18.2/deduplicate_bismark -p --bam ${unsorted_bam} | /src/Bismark-0.18.2/deduplicate_bismark -p --bam ${unsorted_bam} | ||||
| outputdir= dirname ${unsorted_bam} | |||||
| cp $outputdir${sample}_R1_bismark_bt2_pe.deduplicated.bam ./ | |||||
| >>> | >>> | ||||
| runtime { | runtime { | ||||
| docker:docker | docker:docker |
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