更新 'tasks/prepareaa.wdl'

tasks/prepareaa.wdl

@@ -20,7 +20,7 @@ task prepareaa {
     export NCM_HOME=/home/programs/NGSCheckMate-master/
     mkdir -p /home/output/${sample_id}
     cd /home/output/${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}
+    /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}
   
   >>>
 
@@ -31,8 +31,6 @@ task prepareaa {
     dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
   }
   output {
-    Array[File]  cnvkit_result= glob("/home/output/${sample_id}/cnvkit_output/*")
-    Array[File]  AA_result= glob("/home/output/${sample_id}/${sample_id}_AA_results/*")
-    File AA_CNV_SEEDS= "/home/output/${sample_id}/${sample_id}_AA_CNV_SEEDS.bed"
+    Array[File]  AA_result= glob("${sample_id}/*")
   }
 }