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31 lines
975 B
Text
31 lines
975 B
Text
process STAPHOPIASCCMEC {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::staphopia-sccmec=1.0.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/staphopia-sccmec:1.0.0--hdfd78af_0' :
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'quay.io/biocontainers/staphopia-sccmec:1.0.0--hdfd78af_0' }"
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input:
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tuple val(meta), path(fasta)
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output:
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tuple val(meta), path("*.tsv"), emit: tsv
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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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staphopia-sccmec --assembly $fasta $args > ${prefix}.tsv
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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staphopiasccmec: \$(staphopia-sccmec --version 2>&1 | sed 's/^.*staphopia-sccmec //')
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END_VERSIONS
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"""
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}
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