diff --git a/rna-seq.nf b/rna-seq.nf
index 9b851ec8e24f26485bd91c24fd85154afa1c33dc..79a325138a272ffe0866403910c42f88038b949b 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -439,8 +439,9 @@ process parseMetadata {
         fastqReadError_details="**Number of reads do not match for R1 and R2:** there may be a trunkation or mismatch of fastq files"
       fi
     fi
-    if [ "${params.endsForce}" -ne "" ]
+    if [ "${params.endsForce}" != "" ]
     then
+      fastqCountError=false
       fastqReadError=false
       fastqReadError_details=""
     fi