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

@@ -22,6 +22,7 @@ process MLST {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     mlst \\
+        $args \\
         --threads $task.cpus \\
         $fasta \\
         > ${prefix}.tsv