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https://github.com/MillironX/nf-core_modules.git
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41 lines
1.1 KiB
Text
41 lines
1.1 KiB
Text
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process ARIBA_RUN {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/ariba:2.14.6--py39h67e14b5_3':
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'quay.io/biocontainers/ariba:2.14.6--py39h67e14b5_3' }"
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input:
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tuple val(meta), path(reads)
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each path(db)
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output:
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tuple val(meta), path("${prefix}/*"), emit: results
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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def db_name = db.getName().replace('.tar.gz', '')
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"""
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tar -xzvf ${db}
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ariba \\
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run \\
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${db_name}/ \\
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${reads} \\
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${prefix} \\
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$args \\
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--threads $task.cpus
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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ariba: \$(echo \$(ariba version 2>&1) | sed 's/^.*ARIBA version: //;s/ .*\$//')
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END_VERSIONS
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"""
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}
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