kkonganti@105: process MLST {
kkonganti@105:     tag "$meta.id"
kkonganti@105:     label 'process_low'
kkonganti@105: 
kkonganti@105:     module (params.enable_module ? "${params.swmodulepath}${params.fs}mlst${params.fs}2.19.0" : null)
kkonganti@105:     conda (params.enable_conda ? "bioconda::mlst=2.19.0" : null)
kkonganti@105:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@105:         'https://depot.galaxyproject.org/singularity/mlst:2.19.0--hdfd78af_1' :
kkonganti@105:         'quay.io/biocontainers/mlst:2.19.0--hdfd78af_1' }"
kkonganti@105: 
kkonganti@105:     input:
kkonganti@105:     tuple val(meta), path(fasta)
kkonganti@105: 
kkonganti@105:     output:
kkonganti@105:     tuple val(meta), path("*.tsv"), emit: tsv
kkonganti@105:     path "versions.yml"           , emit: versions
kkonganti@105: 
kkonganti@105:     when:
kkonganti@105:     (task.ext.when == null || task.ext.when) && fasta.size() > 0
kkonganti@105: 
kkonganti@105:     script:
kkonganti@105:     def args = task.ext.args ?: ''
kkonganti@105:     def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@105:     """
kkonganti@105:     mlst \\
kkonganti@105:         --threads $task.cpus \\
kkonganti@105:         $args \\
kkonganti@105:         $fasta > ${prefix}.tsv
kkonganti@105: 
kkonganti@105:     cat <<-END_VERSIONS > versions.yml
kkonganti@105:     "${task.process}":
kkonganti@105:         mlst: \$( echo \$(mlst --version 2>&1) | sed 's/mlst //' )
kkonganti@105:     END_VERSIONS
kkonganti@105:     """
kkonganti@105: 
kkonganti@105: }