From bb989a483f9d770888b633991b4ca43443573a00 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 5 Aug 2020 20:23:22 -0500
Subject: [PATCH] Fix raw read count to R1
---
workflow/rna-seq.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index b1cf47e..07d994f 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -914,7 +914,7 @@ process fastqc {
fastqc *.fastq.gz -o .
# count raw reads
- zcat ${fastq[0]} | echo $((`wc -l`/4)) > rawReads.csv
+ zcat *.R1.fastq.gz | echo $((`wc -l`/4)) > rawReads.csv
"""
}
--
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