更新 'tasks/prepareaa.wdl'

tasks/prepareaa.wdl

@@ -11,8 +11,9 @@ task prepareaa {
     set -o pipefail
     set -e 
     export AA_DATA_REPO=/home/data_repo
-    export MOSEKLM_LICENSE_FILE=/home/programs/mosek/8/licenses/mosek.lic
-    source ~/.bashrc
+    export AA_SRC=/home/programs/AmpliconArchitect-master/src
+    export MOSEKLM_LICENSE_FILE=/home/programs/mosek/8/licenses
+    export NCM_HOME=/home/programs/NGSCheckMate-master/
     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}