diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index 3a6918b0fa7a06c281dd7393b62c975ebbd3f396..b279e51b6e217de96cea6ac80e25bfef95e5f00d 100755 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -139,14 +139,13 @@ process parseMetadata { endsManual=\$(python3 ${script_parseMeta} -r ${repRID} -m "${fileMeta}" -p endsManual) echo "LOG: endedness manually detected: \${endsManual}" >>${repRID}.parseMetadata.err - if [ '\${endsMeta}' == 'uk' ] then ends=\${endsManual} - echo "LOG: manual detected endness used" >>${repRID}.parseMetadata.err + echo "LOG: manual detected endness used: \${ends}" >>${repRID}.parseMetadata.err else ends=\${endsMeta} - echo "LOG: metadata endness used" >>${repRID}.parseMetadata.err + echo "LOG: metadata endness used: \${ends}" >>${repRID}.parseMetadata.err fi # Get strandedness metadata