From 797354e0af8d5caa5d3ad2e30b6bd4162d58affd Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 20 Jan 2021 21:15:33 -0600
Subject: [PATCH] Change Single Read to Single End
---
CHANGELOG.md | 1 +
workflow/rna-seq.nf | 4 ++--
2 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3382228..0c1c2a3 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 cac1b87..bdb12e8 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\\": \\".*\\"')
--
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