From 9142b390538283705c084e4d612170972ff60326 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Tue, 10 Dec 2024 12:30:25 +0100
Subject: [PATCH] MEGAHIT: fix single-end input (#7190)

* Fix space to command separated lst

* Put hte join the right place
---
 modules/nf-core/megahit/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/megahit/main.nf b/modules/nf-core/megahit/main.nf
index f6e50f94d43..db0612422bd 100644
--- a/modules/nf-core/megahit/main.nf
+++ b/modules/nf-core/megahit/main.nf
@@ -25,7 +25,7 @@ process MEGAHIT {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def reads_command = meta.single_end || !reads2 ? "-r ${reads1}" : "-1 ${reads1.join(',')} -2 ${reads2.join(',')}"
+    def reads_command = meta.single_end || !reads2 ? "-r ${reads1.join(',')}" : "-1 ${reads1.join(',')} -2 ${reads2.join(',')}"
     """
     megahit \\
         ${reads_command} \\