diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index 57f3e9aad9deccd696ebdd15e18c6a612df29193..e09a1d7f1d2a951dceed0050a4db79bde951cf48 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -238,7 +238,11 @@ process parseMetadata { echo -e "LOG: species metadata parsed: \${species}" >> ${repRID}.parseMetadata.log # get read length metadata - readLength=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experiment}" -p readLength) + readLength=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettings}" -p readLength) + if [ "\${readLength}" == "nan"] + then + readLength="Not Entered" + fi echo -e "LOG: read length metadata parsed: \${readLength}" >> ${repRID}.parseMetadata.log # save design file