From 43f749d8a5fed010a810eef81418ae91b363b6d4 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 28 Feb 2021 15:39:57 -0600
Subject: [PATCH] Add quotes to seqwho error
---
rna-seq.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/rna-seq.nf b/rna-seq.nf
index 550864a..eb7e075 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -812,7 +812,7 @@ process seqwho {
speciesErrorSeqwho=true
speciesErrorSeqwho_details=\$(echo "**Infered species and or sequencing type confidence is low:**\\n")
speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|fastq|Infered species confidence|Infered sequencing type confidence|\\n")
- speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}""|:--|:--:|:--:|\\n)
+ speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|:--|:--:|:--:|\\n")
speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|Read 1|\${speciesConfidenceR1}|\${seqtypeConfidenceR1}|\\n")
if [ "${ends}" == "pe" ]
then
--
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