From 821253a0b706ca39b91246be76e0727be3d34012 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 4 Aug 2020 09:39:15 -0500
Subject: [PATCH] Fix assigned reads extraction
---
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 4be9f4f..bcdcb8b 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -877,7 +877,7 @@ process countData {
echo -e "LOG: counted" >> ${repRID}.countData.log
# extract assigned reads
- assignedReads=grep -m 1 'Assigned' *.countData.summary | grep -oe '\([0-9.]*\)'
+ assignedReads=grep -m 1 'Assigned' *.countData.summary | grep -oe '\\([0-9.]*\\)'
echo -e \${assignedReads} > assignedReads.csv
echo -e "LOG: assigned reads: "\${assignedReads} >> ${repRID}.countData.log
--
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