From 57ac9257a92ef2912163e02425359e2ace8f5aa7 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Mon, 20 Jul 2020 11:29:12 +0200
Subject: [PATCH] Remove now deprecated EAGER flag for HOPS profile

---
 conf/pipeline/eager/shh.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/conf/pipeline/eager/shh.config b/conf/pipeline/eager/shh.config
index c48db8b..777f516 100644
--- a/conf/pipeline/eager/shh.config
+++ b/conf/pipeline/eager/shh.config
@@ -76,7 +76,6 @@ profiles {
       bwaalnn = 0.01
       bwaalnl = 16
       run_bam_filtering = true
-      bam_discard_unmapped = true
       bam_unmapped_type = 'fastq'
       run_metagenomic_screening = true
       metagenomic_tool = 'malt'