更新 'tasks/prepareaa.wdl'

tasks/prepareaa.wdl

@@ -9,9 +9,10 @@ task prepareaa {
   command <<<
     set -o pipefail
     set -e 
-    cd /home/           
-    mkdir /home/output/${sample_name} 
-    /home/programs/PrepareAA-master/PrepareAA.py -s ${sample_name} -t 15 --cnvkit_dir /home/programs/cnvkit.py --sorted_bam ${dedup_bam} --run_AA --ref GRCh38 -o /home/output/${sample_name}/
+    cd /home/input
+    cp ${dedup_bam} ./
+    cp ${dedup_bamindex} ./
+    /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
   
   >>>