diff --git a/CHANGELOG.md b/CHANGELOG.md
index b285b5ddabc459224887f02da2b2ce52274d3772..9d5d0b5f746361ecbf5d25526ba4ef69cedf5d6c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@
 * Update input bag export config to only fetch fastq's that match *[_.]R[1-2].fastq.gz naming convention
 * Remove check for multiple fastq check in parse metadata (redundant and no longer valid)
 * Handle blank submitted endness better
+* Don't use file.csv from inputBag to parse manual endness, use counted from getData
 
 *Known Bugs*
 * Override params (inputBag, fastq, species) aren't checked for integrity
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 770220776ccbb412a92bd2237db1ae6a8dfcc079..c98d141711de8b7718d7e8505658ace116245372 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -344,8 +344,8 @@ process parseMetadata {
     fi
 
     # ganually get endness
-    endsManual=\$(python3 ${script_parseMeta} -r ${repRID} -m "${file}" -p endsManual)
-    echo -e "LOG: endedness manually detected: \${endsManual}" >> ${repRID}.parseMetadata.log
+    endsManual=${fastqCount}
+    echo -e "LOG: endedness manually detected: ${fastqCount}" >> ${repRID}.parseMetadata.log
 
     # get strandedness metadata
     stranded=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettings}" -p stranded)