From e7c65fea29bcce597a1df5c66fb516d88a349277 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 20 Jan 2021 09:30:25 -0600
Subject: [PATCH] Catch error if fastq file error grep
---
workflow/rna-seq.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index e41f42a..5c68c00 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -570,8 +570,8 @@ process fastqc {
# run fastqc
echo -e "LOG: running fastq on raw fastqs" >> ${repRID}.fastqc.log
- fastqcErrorOut=0
- fastqc *.fastq.gz -o . &> fastqc.out || fastqcErrorOut=\$(cat fastqc.out | grep -c 'Failed to process file')
+ fastqc *.fastq.gz -o . &> fastqc.out || true
+ fastqcErrorOut=\$(cat fastqc.out | grep -c 'Failed to process file') || fastqcErrorOut=0
fastqFileError=false
fastqFileError_details=""
if [ "\${fastqcErrorOut}" -ne "0" ]
--
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