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6d6e3a018f
* add module for mykrobe predict and genotyphi parse * Update meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
41 lines
1.2 KiB
Text
41 lines
1.2 KiB
Text
process MYKROBE_PREDICT {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::mykrobe=0.11.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mykrobe:0.11.0--py39h2add14b_1':
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'quay.io/biocontainers/mykrobe:0.11.0--py39h2add14b_1' }"
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input:
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tuple val(meta), path(seqs)
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val species
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output:
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tuple val(meta), path("${prefix}.csv") , emit: csv
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tuple val(meta), path("${prefix}.json"), emit: json
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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"""
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mykrobe \\
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predict \\
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$args \\
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--species $species \\
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--threads $task.cpus \\
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--sample $prefix \\
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--format json_and_csv \\
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--output ${prefix} \\
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--seq $seqs
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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mykrobe: \$(echo \$(mykrobe --version 2>&1) | sed 's/^.*mykrobe v//' )
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END_VERSIONS
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"""
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}
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