From ca8d3a9c64d94c41b7f3e4ac3cef01e1981cef13 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 25 Jan 2021 11:59:09 -0600
Subject: [PATCH] Allow Single Read for backwards compatibility
---
CHANGELOG.md | 2 +-
workflow/rna-seq.nf | 4 ++++
2 files changed, 5 insertions(+), 1 deletion(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0d177da..c0b74db 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,6 @@
# v1.0.3
**User Facing**
-* Endness metadata "Single Read" changed to "Single End" in data-hub, pipeline updated to handle (#110)
+* Endness metadata "Single Read" changed to "Single End" in data-hub, pipeline updated to handle (#110) ("Single Read" still acceptable for backwards compatibility)
**Background**
* Add memory limit (75%) per thread for samtools sort (#108)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index bdb12e8..bce0d20 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -343,6 +343,10 @@ process parseMetadata {
elif [ "\${endsRaw}" == "Paired End" ]
then
endsMeta="pe"
+ elseif [ "\${endsRaw}" == "Single Read" ]
+ # "Single Read" depreciated as of Jan 2021, this option is present for backwards compatibility
+ then
+ endsMeta="se"
elif [ "\${endsRaw}" == "nan" ]
then
endsRaw="_No value_"
--
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