更新 'tasks/prepareaa.wdl'

tasks/prepareaa.wdl

@@ -18,9 +18,9 @@ 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 /home/output/${sample_name}
-    cd /home/output/
-    /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_name}      
+    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} 
+    
   >>>
 
   runtime {
@@ -30,9 +30,9 @@ task prepareaa {
     dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
   }
   output {
-    Array[File]  cnvkit_result= glob("./${sample_name}/cnvkit_output/*")
-    Array[File]  AA_result= glob("./${sample_name}/${sample_name}_AA_results/*")
-    File seed_bed= "./${sample_name}/${sample_name}_AA_CNV_SEEDS.bed"
+
+    Array[File]  AA_result= glob("${sample_name}/*")
+
     
   }
 }