nasty hack to accommodate VEP version for GRCh38

SciLifeLab · Oct 31, 2018 · 2c1f170 · 2c1f170
1 parent 2ada704
commit 2c1f170
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/annotate.nf b/annotate.nf
@@ -215,13 +215,14 @@ process RunVEP {
   script:
   finalannotator = annotator == "snpeff" ? 'merge' : 'vep'
   genome = params.genome == 'smallGRCh37' ? 'GRCh37' : params.genome
+  cache_version = params.genome == 'GRCh38' ? 92 : 91
   """
   /opt/vep/src/ensembl-vep/vep --dir /opt/vep/.vep/  \
   -i ${vcf} \
   -o ${vcf.simpleName}_VEP.ann.vcf \
   --assembly ${genome} \
   --cache \
-	--cache_version 92 \
+	--cache_version ${cache_version} \
   --database \
   --everything \
   --filter_common \