更新 'tasks/prepareaa.wdl'

tasks/prepareaa.wdl

@@ -10,16 +10,17 @@ task prepareaa {
   command <<<
     set -o pipefail
     set -e 
-    export MOSEKPLATFORM=linux64x86
+    #export MOSEKPLATFORM=linux64x86
     #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 LD_LIBRARY_PATH=:/home/programs/mosek/8/tools/platform/linux64x86/bin
+    #export LD_LIBRARY_PATH=:/home/programs/mosek/8/tools/platform/linux64x86/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/
     mkdir -p /home/output/${sample_id}
-    /home/programs/PrepareAA-master/PrepareAA.py -s ${sample_name} -t 20 --cnvkit_dir /home/programs/cnvkit.py --sorted_bam ${dedup_bam} --run_AA --ref GRCh38 -o /home/out/${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}
   
   >>>