From f453a4e321bc982ae66136f893af68ba48ef4a09 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 20 Jan 2021 00:42:27 -0600
Subject: [PATCH] Fix no fastq's present in inputBag
---
workflow/rna-seq.nf | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index f15deb4..9e8f206 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -267,6 +267,10 @@ process getData {
echo -e "LOG: fetched" >> ${repRID}.getData.log
fastqCount=\$(ls *.fastq.gz | wc -l)
+ if [ "\${fastqCount}" == "0" ]
+ then
+ touch dummy.R1.fastq.gz
+ fi
echo "\${fastqCount}" > fastqCount.csv
"""
}
--
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