更新 'tasks/prepareaa.wdl'

tasks/prepareaa.wdl

 task prepareaa {
 
-  File dedup_bam
-  File dedup_bamindex
-  
+  #File dedup_bam
+  #File dedup_bamindex
   String sample_name
   String docker
   String cluster_config
   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}/
+    echo  `pwd` > now_wd
+   # 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}/
   
   >>>
 
     dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
   }
   output {
-    Array[File]  prepareaa_result= glob("/home/output/*")
+    #Array[File]  prepareaa_result= glob("/home/output/*")
+    File now_wd=${now_wd}
   }
 }