From 03fdde8f4895db6fc3a9f4f01f2b60b4840350ec Mon Sep 17 00:00:00 2001
From: Jon Gesell <11574364+jgesell@users.noreply.github.com>
Date: Mon, 5 Jul 2021 11:43:00 -0500
Subject: [PATCH] Update rna-seq.nf
Changed the requested line in the scripts section of rna-seq.nf
---
rna-seq.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/rna-seq.nf b/rna-seq.nf
index 0adcc63..673b863 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" >> ${repRID}.fastqc.log
fastqc *.fastq.gz -o . &> fastqc.out || true
- fastqcErrorOut=\$(cat fastqc.out | grep -c 'Failed to process file') || fastqcErrorOut=0
+ fastqcErrorOut=$(cat fastqc.out | grep -c 'Failed to process') || fastqcErrorOut=0
fastqFileError=false
fastqFileError_details=""
if [ "\${fastqcErrorOut}" -ne "0" ]
--
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