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be798861c6
* add module for abricate * rename abricate/abricate to abricate/run * Update test.yml Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
33 lines
957 B
Text
33 lines
957 B
Text
process ABRICATE_SUMMARY {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1':
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'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }"
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input:
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tuple val(meta), path(reports)
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output:
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tuple val(meta), path("*.txt"), emit: report
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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 ?: "${meta.id}"
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"""
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abricate \\
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--summary \\
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$reports > ${prefix}.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' )
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END_VERSIONS
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"""
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}
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