更新 'tasks/prepareaa.wdl'

tasks/prepareaa.wdl

@@ -18,8 +18,8 @@ task prepareaa {
     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 /cromwell_root/tmp/${sample_name}
-    /home/programs/PrepareAA-master/PrepareAA.py -s ${sample_name} -t 20 --cnvkit_dir /home/programs/cnvkit.py --sorted_bam ${dedup_bam} --run_AA --ref GRCh38 -o /cromwell_root/tmp/${sample_name} 
+    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}
     
   >>>
 
@@ -31,7 +31,7 @@ task prepareaa {
   }
   output {
 
-    Array[File]  AA_result= glob("${sample_name}/*")
+    Array[File]  AA_result= glob("/home/output/${sample_id}/*")
 
     
   }