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839bc6b1ad
* not yet working: add db version to versions.yml * next try: db version number not in versions.yml * Fix amrfinderplus versioning * Update main.nf * Apply suggestions from code review * Update main.nf * Dump version for syncrony with run * Update test.yml * Apply suggestions from code review * add tool and db version to output * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update meta.yml Co-authored-by: James Fellows Yates <jfy133@gmail.com>
60 lines
2.1 KiB
Text
60 lines
2.1 KiB
Text
process AMRFINDERPLUS_RUN {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.30--h6e70893_0':
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'quay.io/biocontainers/ncbi-amrfinderplus:3.10.30--h6e70893_0' }"
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input:
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tuple val(meta), path(fasta)
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path db
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output:
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tuple val(meta), path("${prefix}.tsv") , emit: report
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tuple val(meta), path("${prefix}-mutations.tsv"), emit: mutation_report, optional: true
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path "versions.yml" , emit: versions
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env VER , emit: tool_version
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env DBVER , emit: db_version
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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 is_compressed = fasta.getName().endsWith(".gz") ? true : false
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prefix = task.ext.prefix ?: "${meta.id}"
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organism_param = meta.containsKey("organism") ? "--organism ${meta.organism} --mutation_all ${prefix}-mutations.tsv" : ""
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fasta_name = fasta.getName().replace(".gz", "")
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fasta_param = "-n"
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if (meta.containsKey("is_proteins")) {
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if (meta.is_proteins) {
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fasta_param = "-p"
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}
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}
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"""
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if [ "$is_compressed" == "true" ]; then
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gzip -c -d $fasta > $fasta_name
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fi
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mkdir amrfinderdb
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tar xzvf $db -C amrfinderdb
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amrfinder \\
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$fasta_param $fasta_name \\
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$organism_param \\
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$args \\
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--database amrfinderdb \\
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--threads $task.cpus > ${prefix}.tsv
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VER=\$(amrfinder --version)
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DBVER=\$(echo \$(amrfinder --database amrfinderdb --database_version 2> stdout) | rev | cut -f 1 -d ' ' | rev)
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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amrfinderplus: \$(amrfinder --version)
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amrfinderplus-database: \$(echo \$(echo \$(amrfinder --database amrfinderdb --database_version 2> stdout) | rev | cut -f 1 -d ' ' | rev))
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END_VERSIONS
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"""
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}
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