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15d39f841a
* add amrfinderplus module * Update test.yml * Update main.nf * Update main.nf * Update test.yml * Update test.yml * Update test.yml * Update main.nf * Update meta.yml * Update meta.yml * Update main.nf * Update test.yml * Update test.yml
55 lines
1.7 KiB
Text
55 lines
1.7 KiB
Text
process AMRFINDERPLUS_RUN {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.23" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus%3A3.10.23--h17dc2d4_0':
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'quay.io/biocontainers/ncbi-amrfinderplus:3.10.23--h17dc2d4_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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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 > ${prefix}.tsv
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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amrfinderplus: \$(amrfinder --version)
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END_VERSIONS
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"""
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}
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