更新 'tasks/prepareaa.wdl'

tasks/prepareaa.wdl

@@ -18,10 +18,10 @@ 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/${sample_id}
-    cd /home/output/${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 ${sample_id}
-  
+    #mkdir -p /home/output/${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}
+             
   >>>
 
   runtime {
@@ -32,9 +32,8 @@ task prepareaa {
   }
   output {
     Array[File]  cnvkit_result= glob("${sample_id}/cnvkit_output/*")
-    Array[File]  AA_result= glob("${sample_id}/${sample_id}_AA_results/*")
-    File seed_bed="${sample_id}/${sample_id}_AA_CNV_SEEDS.bed"
-    File mat_expression = "${sample_id}.txt"
+    Array[File]  AA_result= glob("${sample_id}/${sample_name}_AA_results/*")
+    File seed_bed= "${sample_id}/${sample_name}_AA_CNV_SEEDS.bed"
     
   }
 }