From 0a59baf2933982fe6cd6a7379813cc9767ec0e46 Mon Sep 17 00:00:00 2001
From: Petros <70012389+petroslk@users.noreply.github.com>
Date: Mon, 26 Sep 2022 16:48:35 +0200
Subject: [PATCH] Add args to mlst (#1962)

Update main.nf

Add args in main command to allow for parsing of arguments from config file

Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
---
 modules/mlst/main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/mlst/main.nf b/modules/mlst/main.nf
index 65396548..ca86fba8 100644
--- a/modules/mlst/main.nf
+++ b/modules/mlst/main.nf
@@ -22,6 +22,7 @@ process MLST {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     mlst \\
+        $args \\
         --threads $task.cpus \\
         $fasta \\
         > ${prefix}.tsv