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940d7fe9d6
* Move MetaPhlAn3 to a subcommand and add mergemetaphlantables * Add mergemetaphlantables tests * Add mergemetaphlantables to test config * Apply suggestions from code review * Revert now unnecessary input channel name change and now document * Update modules/metaphlan3/mergemetaphlantables/main.nf * Require database directory and more details in description
33 lines
955 B
Text
33 lines
955 B
Text
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0' :
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'quay.io/biocontainers/metaphlan:3.0.12--pyhb7b1952_0' }"
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input:
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path(profiles)
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output:
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tuple path("${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 ?: "merged_abundance_table"
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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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