更新 'tasks/prepareaa.wdl'

tasks/prepareaa.wdl

@@ -10,8 +10,8 @@ task prepareaa {
   command <<<
     set -o pipefail
     set -e 
-    echo export AA_DATA_REPO=/home/data_repo >> ~/.bashrc
-    export MOSEKLM_LICENSE_FILE=/home/programs/mosek/8/licenses/mosek.lic >> ~/.bashrc
+    export AA_DATA_REPO=/home/data_repo
+    export MOSEKLM_LICENSE_FILE=/home/programs/mosek/8/licenses/mosek.lic
     source ~/.bashrc
     mkdir /home/output/${sample_id}
     /home/programs/PrepareAA-master/PrepareAA.py -s ${sample_name} -t 15 --cnvkit_dir /home/programs/cnvkit.py --sorted_bam ${dedup_bam} --run_AA --ref GRCh38 -o /home/output/${sample_id}