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34 lines
971 B
Plaintext
34 lines
971 B
Plaintext
process METAPHLAN3_MERGEMETAPHLANTABLES {
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label 'process_single'
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conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0' :
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'quay.io/biocontainers/metaphlan:3.0.12--pyhb7b1952_0' }"
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input:
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tuple val(meta), path(profiles)
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output:
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tuple val(meta), path("${prefix}.txt") , emit: txt
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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 ?: "${meta.id}"
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"""
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merge_metaphlan_tables.py \\
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$args \\
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-o ${prefix}.txt \\
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${profiles}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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metaphlan3: \$(metaphlan --version 2>&1 | awk '{print \$3}')
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END_VERSIONS
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"""
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}
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