From ddc9ef203573603526ce35eaf4d2c78200ab0681 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 26 Jan 2021 09:03:19 -0600
Subject: [PATCH] Fix getRef use of new spike values
---
workflow/rna-seq.nf | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 75df6fe..4eb3a93 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -1375,7 +1375,7 @@ process uploadExecutionRun {
then
genomeName=\$(echo GRCm${refMoVersion})
fi
- if [ "${spike}" == "yes" ]
+ if [ "${spike}" == "true" ]
then
genomeName=\$(echo \${genomeName}-S)
fi
@@ -1480,10 +1480,10 @@ process getRef {
echo -e "LOG: ERROR - References could not be set!\nSpecies reference found: ${species}" >> ${repRID}.getRef.log
exit 1
fi
- if [ "${spike}" == "yes" ]
+ if [ "${spike}" == "true" ]
then
references=\$(echo \${reference}-S)
- elif [ "${spike}" == "no" ]
+ elif [ "${spike}" == "false" ]
then
reference=\$(echo \${references})
fi
--
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