From eec5b4c5137f85832b2d496b798bccb7e614a206 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 28 Feb 2021 14:56:13 -0600
Subject: [PATCH] Add quotes to seqwho error
---
rna-seq.nf | 8 ++++----
workflow/nextflowConf | 1 -
2 files changed, 4 insertions(+), 5 deletions(-)
delete mode 120000 workflow/nextflowConf
diff --git a/rna-seq.nf b/rna-seq.nf
index 69070d0..550864a 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -811,12 +811,12 @@ process seqwho {
else
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}|Read 1|\${speciesConfidenceR1}|\${seqtypeConfidenceR1}|\\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}"|Read 1|\${speciesConfidenceR1}|\${seqtypeConfidenceR1}|\\n")
if [ "${ends}" == "pe" ]
then
- speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}|Read 2|\${speciesConfidenceR2}|\${seqtypeConfidenceR2}|\\n)
+ speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|Read 2|\${speciesConfidenceR2}|\${seqtypeConfidenceR2}|\\n")
fi
echo -e "LOG: inference error: \${speciesErrorSeqwho_details}" >> ${repRID}.seqwho.log
fi
diff --git a/workflow/nextflowConf b/workflow/nextflowConf
deleted file mode 120000
index 8e5c4cf..0000000
--- a/workflow/nextflowConf
+++ /dev/null
@@ -1 +0,0 @@
-../nextflowConf/
\ No newline at end of file
--
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