更新 'tasks/ASCAT.wdl'

tasks/ASCAT.wdl

@@ -5,6 +5,7 @@ task ASCAT{
     File tumor_bam_index
     File? normal_bam
     File? normal_bam_index
+    File? bed_file
     String gender
     String ref_genome
     String docker
@@ -16,8 +17,14 @@ task ASCAT{
         set -e
         
         out_dir='./'
-         /root/miniconda3/envs/hrd/bin/Rscript /home/ASCAT/ascat.r ${tumor_bam} ${normal_bam} ${sample}'_T' ${sample}'_N' ${sample} WGS $out_dir ${gender} ${ref_genome}
+        
+        if [ ${bed_file} ]; then
+           
+           /root/miniconda3/envs/hrd/bin/Rscript /home/ASCAT/ascat.r ${tumor_bam} ${normal_bam} ${sample}'_T' ${sample}'_N' ${sample} WES $out_dir ${gender} ${ref_genome} ${bed_file}
+        else     
+         	/root/miniconda3/envs/hrd/bin/Rscript /home/ASCAT/ascat.r ${tumor_bam} ${normal_bam} ${sample}'_T' ${sample}'_N' ${sample} WGS $out_dir ${gender} ${ref_genome}
 
+        fi
         ls ./
 
         tar cvf ${sample}.tar ./