From 35ed09b06ec7b87bec0694d6385e8149fd4fe961 Mon Sep 17 00:00:00 2001
From: Michael L Heuer <heuermh@acm.org>
Date: Fri, 5 Feb 2021 11:41:36 -0600
Subject: [PATCH] Fix CI test failure

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

diff --git a/software/minimap2/align/main.nf b/software/minimap2/align/main.nf
index b5cd6712..7af8b45f 100644
--- a/software/minimap2/align/main.nf
+++ b/software/minimap2/align/main.nf
@@ -29,7 +29,7 @@ process MINIMAP2_ALIGN {
     script:
     def software = getSoftwareName(task.process)
     def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def input_reads = meta.single_end ? "-r $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
+    def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}"
     """
     minimap2 \\
         $options.args \\