更新 'tasks/prepareaa.wdl'

tasks/prepareaa.wdl

@@ -9,7 +9,8 @@ task prepareaa {
   command <<<
     set -o pipefail
     set -e 
-    /home/programs/PrepareAA-master/PrepareAA.py -s ${sample_name} -t 15 --cnvkit_dir /home/programs/cnvkit.py --sorted_bam /home/input/${dedup_bam} --run_AA --ref GRCh38 -o /home/output
+    bash /home/run_paa_script.sh
+    /home/programs/PrepareAA-master/PrepareAA.py -s ${sample_name} -t 15 --cnvkit_dir /home/programs/cnvkit.py --sorted_bam /home/input/${dedup_bam} --run_AA --ref GRCh38 -o output
   
   >>>
 
@@ -20,6 +21,6 @@ task prepareaa {
     dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
   }
   output {
-    Array[File]  prepareaa_result= glob("/home/output/*")
+    Array[File]  prepareaa_result= glob("output")
   }
 }