更新 'tasks/prepareaa.wdl'

tasks/prepareaa.wdl

@@ -3,17 +3,18 @@ task prepareaa {
   File dedup_bam
   File dedup_bamindex
   String sample_name
+  String sample_id
   String docker
   String cluster_config
   String disk_size
   command <<<
     set -o pipefail
     set -e 
-    cd /home
-    bash /home/run_paa_script.sh
-    export PATH=$PATH:/home/programs/AmpliconArchitect-master/src/AmpliconArchitect.py
+    echo export AA_DATA_REPO=/home/data_repo >> ~/.bashrc
+    export MOSEKLM_LICENSE_FILE= /home/programs/mosek/8/licenses/mosek.lic>> ~/.bashrc
     source ~/.bashrc
-    /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 ${sample_name}
+    mkdir /home/output/${sample_id}
+    /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_id}
   
   >>>
 
@@ -24,6 +25,6 @@ task prepareaa {
     dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
   }
   output {
-    Array[File]  prepareaa_result= glob("${sample_name}/*")
+    Array[File]  prepareaa_result= glob("/home/output/${sample_id}*")
   }
 }