Don't parse manual ends from file.csv anymore

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 * Remove check for multiple fastq check in parse metadata (redundant and no longer valid)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

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)