linzipeng
6 years ago
1 changed files with 4 additions and 3 deletions
+ 4
- 3
tasks/Dedup.wdl
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| set -o pipefail | set -o pipefail | ||||
| set -e | set -e | ||||
| cp ${unsorted_bam} ./ | cp ${unsorted_bam} ./ | ||||
| input = basename ${unsorted_bam} | |||||
| /src/Bismark-0.18.2/deduplicate_bismark -p --bam ./${input} | |||||
| inputfile = basename ${unsorted_bam} | |||||
| /src/Bismark-0.18.2/deduplicate_bismark -p --bam ./$inputfile | |||||
| >>> | >>> | ||||
| runtime { | runtime { | ||||
| docker:docker | docker:docker | ||||
| } | } | ||||
| output { | output { | ||||
| File Dedup_bam = "${sample}_R1_bismark_bt2_pe.deduplicated.bam" | |||||
| File dedup_bam = "${sample}_R1_bismark_bt2_pe.deduplicated.bam" | |||||
| File dedup_repoet = "${sample}_R1_bismark_bt2_pe.deduplication_report.txt" | |||||
| } | } | ||||
| } | } | ||||
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