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dfbb0bc17c
* update bakta to latest version (v1.4.0) * Update test.yml * remove empty file md5sums * bakta was rebuilt to fix dependencies on bioconda * trigger ci Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
72 lines
2.4 KiB
Text
72 lines
2.4 KiB
Text
process BAKTA {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::bakta=1.4.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bakta:1.4.0--pyhdfd78af_1' :
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'quay.io/biocontainers/bakta:1.4.0--pyhdfd78af_1' }"
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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("${prefix}.tsv") , emit: tsv
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tuple val(meta), path("${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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def proteins_opt = proteins ? "--proteins ${proteins[0]}" : ""
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def prodigal_opt = prodigal_tf ? "--prodigal-tf ${prodigal_tf[0]}" : ""
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"""
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bakta \\
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$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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"${task.process}":
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bakta: \$( echo \$(bakta --version 2>&1) | sed 's/^.*bakta //' )
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END_VERSIONS
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"""
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stub:
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prefix = task.ext.prefix ?: "${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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touch ${prefix}.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bakta: \$( 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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