Fixbug: Syntax

tasks/VEP.wdl

@@ -42,7 +42,7 @@ task VEP {
     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"
-      cp ${vcf} ${sample_id}.tmp.vcf
+      cp ${vcf} ${sample_id}.tmp1.vcf
     else
       SAMPLE_vcf2maf="--tumor-id $tumor_id"
       # Add a column and remove it after vcf2vcf
@@ -62,7 +62,7 @@ task VEP {
       cp ${sample_id}.tmp2.vcf ${basename}.norm.vcf
     else
       cut -f 1,2,3,4,5,6,7,8,9,10 ${sample_id}.tmp2.vcf > ${basename}.norm.vcf
-    
+    fi
 
     # VEP annotation
     echo "VEP annotation..."