From 3b6afce4406917f7b715ff03ef53591e8e443c23 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 19 Jan 2021 21:31:06 -0600
Subject: [PATCH] Make dummy fastqc output if fail
---
workflow/rna-seq.nf | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index e9e74d6..f9c9b3a 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -558,14 +558,15 @@ process fastqc {
# run fastqc
echo -e "LOG: running fastq on raw fastqs" >> ${repRID}.fastqc.log
- fastqc *.fastq.gz -o . 2> fastqcErrorOut
- fastqcErrorOut=\$(echo \${fastqcErrorOut} | grep -o 'Failed to process file')
+ fastqc *.fastq.gz -o . 2> fastqcErrorOut.txt
+ fastqcErrorOut=\$(cat fastqcErrorOut.txt | grep -o 'Failed to process file')
fastqFileError=false
fastqFileError_details=""
if [ "\${fastqcErrorOut}" != "" ]
then
fastqFileError=true
fastqFileError_details="**There is an error with the structure of the fastq**"
+ touch dummy_fastqc.zip
fi
# count raw reads
--
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