From b78a4a456762a4c59fd5023e70f36a27f76d4a97 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Tue, 8 Mar 2022 15:56:23 +0100
Subject: [PATCH] Fix for Maxbin2 emitting input files (#1376)

* fix: remove left-over unnecessary code

* Fix accidently emitting input

* Fix tests
---
 modules/maxbin2/main.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/maxbin2/main.nf b/modules/maxbin2/main.nf
index 7b818d00..a48df43f 100644
--- a/modules/maxbin2/main.nf
+++ b/modules/maxbin2/main.nf
@@ -29,8 +29,9 @@ process MAXBIN2 {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def associate_files = reads ? "-reads $reads" : "-abund $abund"
     """
+    mkdir input/ && mv $contigs input/
     run_MaxBin.pl \\
-        -contig $contigs \\
+        -contig input/$contigs \\
         $associate_files \\
         -thread $task.cpus \\
         $args \\