diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 6c3622b2f7b94baec7b8a906fe2dd0dcef59c4d0..21c77a09555cabf75011ceab149d3bed31f88e34 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -140,11 +140,11 @@ process parseMetadata {
     echo "LOG: endedness manually detected: \${endsManual}" >>${repRID}.parseMetadata.err
 
     # Get strandedness metadata
-    stranded=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p stranded)
+    stranded=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p stranded -e \${endsManual})
     echo "LOG: strandedness metadata parsed: \${stranded}" >>${repRID}.parseMetadata.err
     
     # Get spike-in metadata
-    spike=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p spike -e \${endsManual})
+    spike=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p spike)
     echo "LOG: spike-in metadata parsed: \${spike}" >>${repRID}.parseMetadata.err
     
     # Get species metadata