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1 process MLST {
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2 tag "$meta.id"
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3 label 'process_micro'
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}mlst${params.fs}2.23.0" : null)
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6 conda (params.enable_conda ? "conda-forge::perl bioconda::mlst=2.23.0" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/mlst:2.23.0--hdfd78af_1' :
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9 'quay.io/biocontainers/mlst:2.23.0--hdfd78af_1' }"
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10
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11 input:
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12 tuple val(meta), path(fasta)
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13
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14 output:
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15 tuple val(meta), path("*.tsv"), emit: tsv
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16 path "versions.yml" , emit: versions
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17
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18 when:
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19 (task.ext.when == null || task.ext.when) && fasta.size() > 0
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20
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21 script:
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22 def args = task.ext.args ?: ''
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23 def prefix = task.ext.prefix ?: "${meta.id}"
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24 """
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25 mlst \\
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26 --threads $task.cpus \\
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27 --label $prefix \\
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28 $args \\
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29 $fasta > ${prefix}.tsv
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30
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31 cat <<-END_VERSIONS > versions.yml
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32 "${task.process}":
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33 mlst: \$( echo \$(mlst --version 2>&1) | sed 's/mlst //' )
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34 END_VERSIONS
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35 """
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36
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37 } |
