diff --git a/workflow/main.nf b/workflow/main.nf
index 31ae9f44f40fba6dec76873d2a37be6573d5575c..785d7aee2762adacacd263683ac20bba5a0ff1fe 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -53,9 +53,9 @@ if (params.astrocyte) {
 }
 
 // Check inputs
-if(params.bwa) {
-  bwa= Channel
-    .fromPath(params.bwa)
+if(params.bwaIndex) {
+  bwaIndex = Channel
+    .fromPath(params.bwaIndex)
     .ifEmpty { exit 1, "BWA index not found: ${params.bwaIndex}" }
 } else {
   exit 1, "No reference genome specified."