test

tasks/VEP.wdl

@@ -21,6 +21,8 @@ task VEP {
     nt=$(nproc)
 
     source /etc/profile
+    echo ${sample_id}
+    echo ${basename}
 
     #awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > ${sample_id}.vcf
 
@@ -36,7 +38,7 @@ task VEP {
     # Judge the SAMPLE info of vcf file
     tumor_id=`awk -F'\t' '{if($1~"^#CHROM"){print $10}}' ${vcf}`
     normal_id=`awk -F'\t' '{if($1~"^#CHROM"){print $11}}' ${vcf}`
-    
+
     if [ $normal_id ]; then
       SAMPLE_vcf2maf="--tumor-id $tumor_id --normal-id $normal_id"
       SAMPLE_vcf2vcf="--vcf-tumor-id $tumor_id --vcf-normal-id $normal_id"