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Add args to mlst (#1962)

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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>
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Petros 2022-09-26 16:48:35 +02:00 committed by GitHub
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modules/mlst/main.nf
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@ -22,6 +22,7 @@ process MLST {
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
""" """
mlst \\ mlst \\
$args \\
--threads $task.cpus \\ --threads $task.cpus \\
$fasta \\ $fasta \\
> ${prefix}.tsv > ${prefix}.tsv