From d7189017aab37b09c399f5cc3772582439eecf74 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 4 Aug 2020 13:07:06 -0500
Subject: [PATCH] Fix assigned read 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 9579ce1..0c7285b 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
- grep -m 1 'Assigned' *.countData.summary | grep -oe '\\([0-9.]*\\)') > assignedReads.csv
+ grep -m 1 'Assigned' *.countData.summary | grep -oe '\\([0-9.]*\\)' > assignedReads.csv
# calculate TPM from the resulting countData table
echo -e "LOG: calculating TPM with R" >> ${repRID}.countData.log
--
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