更新 'tasks/prepareaa.wdl'

tasks/prepareaa.wdl

@@ -10,11 +10,14 @@ task prepareaa {
   command <<<
     set -o pipefail
     set -e 
+    export MOSEKPLATFORM=linux64x86
+    export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/programs/mosek/8/tools/platform//bin
+    export LD_LIBRARY_PATH=:/home/programs/mosek/8/tools/platform//bin
     export AA_DATA_REPO=/home/data_repo
     export AA_SRC=/home/programs/AmpliconArchitect-master/src
     export MOSEKLM_LICENSE_FILE=/home/programs/mosek/8/licenses
     export NCM_HOME=/home/programs/NGSCheckMate-master/
-    /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}
+    /home/programs/PrepareAA-master/PrepareAA.py -s ${sample_name} -t 20 --cnvkit_dir /home/programs/cnvkit.py --sorted_bam ${dedup_bam} --run_AA --ref GRCh38 -o /home/out/${sample_id}
   
   >>>
 
@@ -25,6 +28,6 @@ task prepareaa {
     dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
   }
   output {
-    Array[File]  prepareaa_result= glob("${sample_id}/*")
+    Array[File]  prepareaa_result= glob("/home/out/${sample_id}/*")
   }
 }