diff --git a/nextflow/nf_modules/check_VCF.nf b/nextflow/nf_modules/check_VCF.nf
index 8e54559d6..bb2876255 100644
--- a/nextflow/nf_modules/check_VCF.nf
+++ b/nextflow/nf_modules/check_VCF.nf
@@ -20,7 +20,7 @@ process checkVCF {
   errorStrategy 'ignore'
 
   input:
-  tuple val(meta), path(vcf), path(vep_config)
+  tuple val(meta), path(vcf), path(vcf_index), path(vep_config)
   
   output:
   tuple val(meta), path("*.gz", includeInputs: true), path ("*.gz.{tbi,csi}", includeInputs: true), path(vep_config)
diff --git a/nextflow/workflows/run_vep.nf b/nextflow/workflows/run_vep.nf
index 72c2118fa..11b64aa52 100644
--- a/nextflow/workflows/run_vep.nf
+++ b/nextflow/workflows/run_vep.nf
@@ -135,7 +135,9 @@ workflow {
         // NOTE: csi is default unless a tbi index already exists
         meta.index_type = file(vcf + ".tbi").exists() ? "tbi" : "csi"
 
-        [ meta, vcf, vep_config ]
+        vcf_index = vcf + ".${meta.index_type}"
+
+        [ meta, vcf, vcf_index, vep_config ]
     }
     .set{ ch_input }