diff --git a/rna-seq.nf b/rna-seq.nf
index f4f19d313b24c0ca24bbd1ae12b68f813cf61dee..5c2c96d38390cc331a67ab580440178a172279cb 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -273,6 +273,7 @@ process getData {
       echo -e "LOG: fetched" >> ${repRID}.getData.log
     else
       echo -e "LOG: fastq override detected, not fetching fastqs" >> ${repRID}.getData.log
+      fastqCount="0"
     fi
 
     if [ "\${fastqCount}" == "0" ]