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58ee946ca6
* gappa/examineassign: Explicitly output two optional files * Check versions.yml for md5 sum instead
43 lines
1.5 KiB
Text
43 lines
1.5 KiB
Text
process GAPPA_EXAMINEASSIGN {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gappa:0.8.0--h9a82719_0':
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'quay.io/biocontainers/gappa:0.8.0--h9a82719_0' }"
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input:
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tuple val(meta), path(jplace)
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path taxonomy
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output:
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tuple val(meta), path("./.") , emit: examineassign
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tuple val(meta), path("*profile.tsv") , emit: profile
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tuple val(meta), path("*labelled_tree.newick"), emit: labelled_tree
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tuple val(meta), path("*per_query.tsv") , emit: per_query, optional: true
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tuple val(meta), path("*krona.profile") , emit: krona , optional: true
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tuple val(meta), path("*sativa.tsv") , emit: sativa , optional: true
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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 ?: "${meta.id}"
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"""
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gappa \\
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examine assign \\
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$args \\
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--threads $task.cpus \\
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--jplace-path $jplace \\
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--taxon-file $taxonomy \\
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--file-prefix ${prefix}.
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gappa: \$(echo \$(gappa --version 2>&1 | sed 's/v//' ))
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END_VERSIONS
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"""
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}
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