更新 'tasks/manta.wdl'

tasks/manta.wdl

@@ -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}