From 884c4658b87fda9b7ff1a830a9b2def25041557e Mon Sep 17 00:00:00 2001
From: Anders Goncalves da Silva <andersgs@gmail.com>
Date: Wed, 10 Feb 2021 10:00:22 -0800
Subject: [PATCH] Make mpileup saving optional

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 software/ivar/consensus/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/software/ivar/consensus/main.nf b/software/ivar/consensus/main.nf
index 54ea8f8a..bf326205 100644
--- a/software/ivar/consensus/main.nf
+++ b/software/ivar/consensus/main.nf
@@ -36,7 +36,7 @@ process IVAR_CONSENSUS {
         -aa -A -d 0 -Q 0 \\
         $options.args2 \\
         $bam | \\
-        tee ${prefix}_mpileup.txt | \\
+        $save_mpileup \\
         ivar consensus \\
         $options.args \\
         -p $prefix