From 5b271a2eb109cdfff86c58d0d96a949a675188ae Mon Sep 17 00:00:00 2001
From: Jon Gesell <11574364+jgesell@users.noreply.github.com>
Date: Mon, 5 Jul 2021 12:07:14 -0500
Subject: [PATCH] Corrected missing escape character.
---
rna-seq.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/rna-seq.nf b/rna-seq.nf
index 673b863..159805d 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -634,7 +634,7 @@ process fastqc {
# run fastqc
echo -e "LOG: running fastq on raw fastqs" >> ${repRID}.fastqc.log
fastqc *.fastq.gz -o . &> fastqc.out || true
- fastqcErrorOut=$(cat fastqc.out | grep -c 'Failed to process') || fastqcErrorOut=0
+ fastqcErrorOut=\$(cat fastqc.out | grep -c 'Failed to process') || fastqcErrorOut=0
fastqFileError=false
fastqFileError_details=""
if [ "\${fastqcErrorOut}" -ne "0" ]
--
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