From 3235c1c47af83e42616dbb13e8718d91ef396add Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 29 Jan 2021 10:49:07 -0600
Subject: [PATCH] Fix bool spike override in getRef
---
workflow/rna-seq.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index fffa464..dbcfbc0 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -1539,10 +1539,10 @@ process getRef {
echo -e "LOG: ERROR - References could not be set!\nSpecies reference found: ${species}" >> ${repRID}.getRef.log
exit 1
fi
- if [ "${spike}" == "t" ]
+ if [ "${spike}" == "true" ]
then
references=\$(echo \${reference}-S)
- elif [ "${spike}" == "f" ]
+ elif [ "${spike}" == "false" ]
then
reference=\$(echo \${references})
fi
--
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