From 069836627b395c0353ca3672ec5abac536cd2ee9 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 4 Aug 2020 09:45:06 -0500
Subject: [PATCH] Remove intermediate bash variables
---
workflow/rna-seq.nf | 5 +----
1 file changed, 1 insertion(+), 4 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index dc0a8d1..9c936c6 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -877,10 +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.]*\\)')
- echo -e \${assignedReads} > assignedReads.csv
- echo -e "LOG: assigned reads: "\${assignedReads} >> ${repRID}.countData.log
-
+ 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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