1 changed files with 2 additions and 2 deletions
+ 2
- 2
tasks/manta.wdl
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| @@ -15,7 +15,7 @@ task manta_calling{ | |||
| String out_dir = "${sample_id}_result" | |||
| command <<< | |||
| set -exo pipefail | |||
| cpu=$(nproc) | |||
| nt=$(nproc) | |||
| /home/biosoft/manta-1.6.0.centos6_x86_64/bin/configManta.py \ | |||
| --normalBam ${normal_bam} \ | |||
| --tumorBam ${tumour_bam} \ | |||
| @@ -24,7 +24,7 @@ task manta_calling{ | |||
| ls ${out_dir} | |||
| python2.7 ${out_dir}/runWorkflow.py -m local -j ${cpu} | |||
| python2.7 ${out_dir}/runWorkflow.py -m local -j $nt | |||
| ls ${out_dir} | |||
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