From d633e19c91c31fcddbfcad47b7519123cb77493c Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 2 Mar 2021 11:38:37 -0600
Subject: [PATCH] Set fastq count temporarily to zero if overridden

---
 rna-seq.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/rna-seq.nf b/rna-seq.nf
index f4f19d3..5c2c96d 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -273,6 +273,7 @@ process getData {
       echo -e "LOG: fetched" >> ${repRID}.getData.log
     else
       echo -e "LOG: fastq override detected, not fetching fastqs" >> ${repRID}.getData.log
+      fastqCount="0"
     fi
 
     if [ "\${fastqCount}" == "0" ]
-- 
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