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46 lines
1.6 KiB
Text
46 lines
1.6 KiB
Text
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process MOBSUITE_RECON {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::mob_suite=3.0.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mob_suite%3A3.0.3--pyhdfd78af_0':
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'quay.io/biocontainers/mob_suite:3.0.3--pyhdfd78af_0' }"
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input:
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tuple val(meta), path(fasta)
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output:
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tuple val(meta), path("results/chromosome.fasta") , emit: chromosome
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tuple val(meta), path("results/contig_report.txt") , emit: contig_report
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tuple val(meta), path("results/plasmid_*.fasta") , emit: plasmids , optional: true
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tuple val(meta), path("results/mobtyper_results.txt"), emit: mobtyper_results, 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 ?: "${meta.id}"
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def is_compressed = fasta.getName().endsWith(".gz") ? true : false
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def fasta_name = fasta.getName().replace(".gz", "")
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"""
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if [ "$is_compressed" == "true" ]; then
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gzip -c -d $fasta > $fasta_name
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fi
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mob_recon \\
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--infile $fasta_name \\
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$args \\
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--num_threads $task.cpus \\
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--outdir results \\
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--sample_id $prefix
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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mobsuite: \$(echo \$(mob_recon --version 2>&1) | sed 's/^.*mob_recon //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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