From 4e00c765304cdbea96acd7c85d65fddf4fffff23 Mon Sep 17 00:00:00 2001
From: Nicholas Minor <nrminor@wisc.edu>
Date: Wed, 6 Nov 2024 14:36:08 -0600
Subject: [PATCH] fixing a typo in the minimap module

---
 modules/minimap2.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/minimap2.nf b/modules/minimap2.nf
index af7ed58..86660c3 100644
--- a/modules/minimap2.nf
+++ b/modules/minimap2.nf
@@ -14,7 +14,7 @@ process ALIGN_WITH_PRESET {
 
     script:
     preset = params.platform == "ont" ? "map-ont" : "sr"
-    secondary = params.secondary ? "no" : "ues"
+    secondary = params.secondary ? "no" : "yes"
     """
     minimap2 \
     --secondary=${secondary} \