更新 'tasks/prepareaa.wdl'

tasks/prepareaa.wdl

@@ -17,10 +17,11 @@ task prepareaa {
     export AA_DATA_REPO=/home/data_repo
     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 -p /home/output/${sample_id}
-    /home/programs/PrepareAA-master/PrepareAA.py -s ${sample_name} -t 20 --cnvkit_dir /home/programs/cnvkit.py --sorted_bam ${dedup_bam} --run_AA --ref GRCh38 -o /home/output/${sample_id}
-    
+    export NCM_HOME=/home/programs/NGSCheckMate-master/ 
+                
+    mkdir -p /cromwell_root/tmp/aaresult
+    cd /cromwell_root/tmp/aaresult 
+    /home/programs/PrepareAA-master/PrepareAA.py -s ${sample_name} -t 20 --cnvkit_dir /home/programs/cnvkit.py --sorted_bam ${dedup_bam} --run_AA --ref GRCh38 -o ${sample_id}
   >>>
 
   runtime {
@@ -31,7 +32,7 @@ task prepareaa {
   }
   output {
 
-    Array[File]  AA_result= glob("${sample_id}/*")
+    Array[File]  AA_result= glob("/cromwell_root/tmp/aaresult/*")
 
     
   }