Update: VEP

tasks/VEP.wdl

@@ -9,7 +9,7 @@ task VEP {
   String fasta
   String vep_path
   File cache
-  String ncbi_build
+  String hg
   String species
   String vcf2maf_path
   String docker
@@ -24,6 +24,12 @@ task VEP {
 
     awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > ${basename}.PASS.vcf
     
+    # Define ncbi_build
+    if [ hg == "hg19" ]; then
+      ncbi_build="GRCh37"
+    elif [ hg == "hg38" ]; then
+      ncbi_build="GRCh38"
+    
     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}"