From b95cdee776d670a0763313964ee2901882044600 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 20 Jan 2021 00:34:18 -0600
Subject: [PATCH] Fix file structure error detection
---
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 f890b82..f15deb4 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -564,10 +564,11 @@ process fastqc {
# run fastqc
echo -e "LOG: running fastq on raw fastqs" >> ${repRID}.fastqc.log
fastqcErrorOut=false
- fastqc *.fastq.gz -o . || fastqcErrorOut=true
+ fastqc *.fastq.gz -o . &> fastqc.out || :
+ fastqcErrorOut=\$(cat fastqc.out | grep -c 'Failed to process file')
fastqFileError=false
fastqFileError_details=""
- if [ "\${fastqcErrorOut}" == "true" ]
+ if [ "\${fastqcErrorOut}" -gt "0" ]
then
fastqFileError=true
fastqFileError_details="**There is an error with the structure of the fastq**"
--
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