diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index fffa4644bc4b2bea6d7207776920f6fbb606b44c..dbcfbc0e88f9513ce65749e9a9bca8d0722b23f1 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -1539,10 +1539,10 @@ process getRef {
       echo -e "LOG: ERROR - References could not be set!\nSpecies reference found: ${species}" >> ${repRID}.getRef.log
       exit 1
     fi
-    if [ "${spike}" == "t" ]
+    if [ "${spike}" == "true" ]
     then
       references=\$(echo \${reference}-S)
-    elif [ "${spike}" == "f" ]
+    elif [ "${spike}" == "false" ]
     then
       reference=\$(echo \${references})
     fi