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29c669766d
* add bakta module * Update main.nf * Update main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
77 lines
2.8 KiB
Text
77 lines
2.8 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process BAKTA {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::bakta=1.2.2" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/bakta:1.2.2--pyhdfd78af_0"
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} else {
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container "quay.io/biocontainers/bakta:1.2.2--pyhdfd78af_0"
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}
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input:
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tuple val(meta), path(fasta)
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path db
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path proteins
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path prodigal_tf
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output:
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tuple val(meta), path("${prefix}.embl") , emit: embl
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tuple val(meta), path("${prefix}.faa") , emit: faa
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tuple val(meta), path("${prefix}.ffn") , emit: ffn
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tuple val(meta), path("${prefix}.fna") , emit: fna
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tuple val(meta), path("${prefix}.gbff") , emit: gbff
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tuple val(meta), path("${prefix}.gff3") , emit: gff
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tuple val(meta), path("${prefix}.hypotheticals.tsv"), emit: hypotheticals_tsv
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tuple val(meta), path("${prefix}.hypotheticals.faa"), emit: hypotheticals_faa
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tuple val(meta), path("${prefix}.tsv") , emit: tsv
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path "versions.yml" , emit: versions
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script:
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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def proteins_opt = proteins ? "--proteins ${proteins[0]}" : ""
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def prodigal_opt = prodigal_tf ? "--prodigal-tf ${prodigal_tf[0]}" : ""
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"""
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bakta \\
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$options.args \\
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--threads $task.cpus \\
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--prefix ${prefix} \\
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--db $db \\
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$proteins_opt \\
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$prodigal_tf \\
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$fasta
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( echo \$(bakta --version 2>&1) | sed 's/^.*bakta //' )
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END_VERSIONS
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"""
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stub:
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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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touch ${prefix}.embl
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touch ${prefix}.faa
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touch ${prefix}.ffn
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touch ${prefix}.fna
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touch ${prefix}.gbff
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touch ${prefix}.gff3
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touch ${prefix}.hypotheticals.tsv
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touch ${prefix}.hypotheticals.faa
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touch ${prefix}.tsv
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( echo \$(bakta --version 2>&1) | sed 's/^.*bakta //' )
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END_VERSIONS
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"""
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}
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