Resolve "Astrocyte fixes"

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Closes #40 (closed)

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."