diff --git a/CHANGELOG.md b/CHANGELOG.md index 3382228f8fdee34882c81df36e2773641a82a604..0c1c2a3d9606e7f99ae4fc0a19e41882eb5606b0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,6 @@ # v1.0.3 **User Facing** +* Endness metadata "Single Read" changed to "Single End" in data-hub, pipeline updated to handle **Background** * Add memory limit (75%) per thread for samtools sort (#108) diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index cac1b878d53b22685e973560cfc1c01ac0713e52..bdb12e8e5a2c3c82060ee7c74a5cd03ce9119372 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -337,7 +337,7 @@ process parseMetadata { # get endedness metadata endsRaw=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettings}" -p endsMeta) echo -e "LOG: endedness metadata parsed: \${endsRaw}" >> ${repRID}.parseMetadata.log - if [ "\${endsRaw}" == "Single Read" ] + if [ "\${endsRaw}" == "Single End" ] then endsMeta="se" elif [ "\${endsRaw}" == "Paired End" ] @@ -2021,7 +2021,7 @@ process uploadQC { end="Paired End" elif [ "${ends}" == "se" ] then - end="Single Read" + end="Single End" fi cookie=\$(cat credential.json | grep -A 1 '\\"${source}\\": {' | grep -o '\\"cookie\\": \\".*\\"')