更新 'tasks/prepareaa.wdl'

tasks/prepareaa.wdl

@@ -19,9 +19,10 @@ task prepareaa {
     export MOSEKLM_LICENSE_FILE=/home/programs/mosek/8/licenses
     export NCM_HOME=/home/programs/NGSCheckMate-master/ 
                 
-    mkdir -p /cromwell_root/tmp/aaresult
+    mkdir -p /home/output/${sample_id}
+    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_id}
-    cp -r ${sample_id}  /cromwell_root/tmp/aaresult/         
+    find . -depth > fileList.txt
   >>>
 
   runtime {
@@ -32,7 +33,10 @@ task prepareaa {
   }
   output {
 
-    Array[File]  AA_result= glob("/cromwell_root/tmp/aaresult/*")
+      File fileList = "fileList.txt"
+      Array[File]  cnvkit_output= glob("${sample_id}/cnvkit_output/*")
+      Array[File]  aa_result= glob("${sample_id}/${sample_id}_AA_results/*")
+      File seedbed = "${sample_id}/${sample_id}_AA_CNV_SEEDS.bed"
 
     
   }