Fixbug: vcf2vcf parameter

tasks/VEP.wdl

@@ -29,9 +29,11 @@ task VEP {
     # Judge the SAMPLE info of vcf file
     ncol=`awk -F'\t' '{if($1!~"^#"){print NF}}' ${sample_id}.vcf | uniq`
     if [ $ncol -lt 11 ]; then
-      SAMPLE="--tumor-id ${tumor_id} --normal-id ${normal_id}"
+      SAMPLE_vcf2maf="--tumor-id ${tumor_id} --normal-id ${normal_id}"
+      SAMPLE_vcf2vcf="--vcf-tumor-id ${tumor_id} --vcf-normal-id ${normal_id}"
     else
-      SAMPLE="--tumor-id ${sample_id}"
+      SAMPLE_vcf2maf="--tumor-id ${sample_id}"
+      SAMPLE_vcf2vcf="--vcf-tumor-id ${sample_id}"
     fi
 
     # Set the buffer_size based on the data size
@@ -75,7 +77,7 @@ task VEP {
     # vcf2vcf: transfer into a standardized format
     perl ${vcf2maf_path}/vcf2vcf.pl \
     --input-vcf ${sample_id}.vcf --output-vcf ${basename}.norm.vcf \
-    $SAMPLE \
+    $SAMPLE_vcf2vcf \
     --ref-fasta ${ref_dir}/${fasta}
 
     # VEP annotation
@@ -93,7 +95,7 @@ task VEP {
     perl ${vcf2maf_path}/vcf2maf.pl \
     --inhibit-vep \
     --input-vcf ${basename}.vep.vcf --output-maf ${basename}.maf \
-    $SAMPLE \
+    $SAMPLE_vcf2maf \
     --ref-fasta ${ref_dir}/${fasta} \
     --ncbi-build ${ncbi_build} \
     --species ${species} \