Update: vcf2maf_ID

tasks/VEP.wdl

@@ -23,6 +23,13 @@ task VEP {
     nt=$(nproc)
 
     awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > ${basename}.PASS.vcf
+    ncol=`awk -F'\t' '{if($1!~"^#"){print NF}}' ${basename}.PASS.vcf | uniq`
+    
+    if [ $ncol -lt 11 ]; then
+      vcf2maf_ID="--tumor-id ${tumor_id} --normal-id ${normal_id}"
+    else
+      vcf2maf_ID="--tumor-id ${tumor_id}"
+    fi
 
     # Extract the BND variants from VCF
     # awk -F'\t' '{if(($1~"^#")||($8!~".*SVTYPE=BND.*")){print $0}}' ${sample_id}.PASS.vcf > ${sample_id}.PASS.vcf2maf.vcf
@@ -58,7 +65,7 @@ task VEP {
     perl ${vcf2maf_path}/vcf2maf.pl \
     --inhibit-vep \
     --input-vcf ${basename}.PASS.vep.vcf --output-maf ${basename}.PASS.maf \
-    --tumor-id ${tumor_id} --normal-id ${normal_id} \
+    $vcf2maf_ID \
     --ref-fasta ${ref_dir}/${fasta} \
     --vep-fork $nt
   >>>