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https://github.com/MillironX/nf-core_modules.git
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45 lines
1.2 KiB
Text
45 lines
1.2 KiB
Text
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def VERSION = '1.0.1' // Version information not provided by tool on CLI
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process HPSUISSERO {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::hpsuissero=1.0.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/hpsuissero%3A1.0.1--hdfd78af_0':
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'quay.io/biocontainers/hpsuissero:1.0.1--hdfd78af_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("*.tsv"), emit: tsv
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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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HpsuisSero.sh \\
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-i $fasta_name \\
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-o ./ \\
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-s $prefix \\
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-x fasta \\
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-t $task.cpus
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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hpsuissero: $VERSION
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END_VERSIONS
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"""
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}
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