diff --git a/workflow/main.nf b/workflow/main.nf
index b0d60c637fed7a6dc904affd2a45c8b96021bf09..ca8736febb01b9ecc02a9376db5be290bdcefb95 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -56,6 +56,7 @@ readsList = Channel
   .collectFile( name: 'fileList.tsv', newLine: true )
 
 // Define regular variables
+pairedEnd = params.pairedEnd
 designFile = params.designFile
 genomeSize = params.genomeSize
 genome = params.genome