更新 'tasks/prepareaa.wdl'

tasks/prepareaa.wdl

@@ -9,8 +9,11 @@ task prepareaa {
   command <<<
     set -o pipefail
     set -e 
+    cd /home
     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
+    export PATH=$PATH:/home/programs/AmpliconArchitect-master/src/AmpliconArchitect.py
+    source ~/.bashrc
+    /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 ${sample_name}
   
   >>>
 
@@ -21,6 +24,6 @@ task prepareaa {
     dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
   }
   output {
-    Array[File]  prepareaa_result= glob("output")
+    Array[File]  prepareaa_result= glob("${sample_name}/*")
   }
 }