diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index d45ae8be72cce5339b50e24f9b91cfc737807684..3178a3335771a6427f2bac7ce77a469656ab3c98 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -344,7 +344,11 @@ process parseMetadata {
     fi
 
     # ganually get endness
-    endsManual=${fastqCount}
+    if [ "${fastqCount}" == "1" ]
+      endsManual="se"
+    else
+      endsManual="pe"
+    fi
     echo -e "LOG: endedness manually detected: ${fastqCount}" >> ${repRID}.parseMetadata.log
 
     # get strandedness metadata