linzipeng
6 years ago
1 changed files with 2 additions and 1 deletions
+ 2
- 1
tasks/Dedup.wdl
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| set -e | set -e | ||||
| /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} | outputdir= dirname ${unsorted_bam} | ||||
| cp ${outputdir} ./ | |||||
| bam= "${sample}_R1_bismark_bt2_pe.deduplicated.bam" | |||||
| cp ${outputdir}/${bam} ./ | |||||
| >>> | >>> | ||||
| runtime { | runtime { | ||||
| docker:docker | docker:docker |
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