mirror of
https://github.com/MillironX/nf-core_modules.git
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43 lines
1.4 KiB
Text
43 lines
1.4 KiB
Text
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process KAT_HIST {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::kat=2.4.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/kat:2.4.2--py38hfc5f9d8_2':
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'quay.io/biocontainers/kat:2.4.2--py38hfc5f9d8_2' }"
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input:
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path("*.hist") , emit: hist
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tuple val(meta), path("*.hist.dist_analysis.json"), emit: json
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tuple val(meta), path("*.png") , emit: png , optional: true
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tuple val(meta), path("*.ps") , emit: ps , optional: true
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tuple val(meta), path("*.pdf") , emit: pdf , optional: true
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tuple val(meta), path("*-hash.jf*") , emit: jellyfish_hash, optional: true
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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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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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kat hist \\
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--threads $task.cpus \\
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--output_prefix ${prefix}.hist \\
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$args \\
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$reads
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ls -l
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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kat: \$( kat hist --version | sed 's/kat //' )
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END_VERSIONS
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"""
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}
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