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38 lines
1.1 KiB
Text
38 lines
1.1 KiB
Text
process SEQSERO2 {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::seqsero2=1.2.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/seqsero2:1.2.1--py_0' :
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'quay.io/biocontainers/seqsero2:1.2.1--py_0' }"
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input:
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tuple val(meta), path(seqs)
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output:
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tuple val(meta), path("results/*_log.txt") , emit: log
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tuple val(meta), path("results/*_result.tsv"), emit: tsv
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tuple val(meta), path("results/*_result.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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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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SeqSero2_package.py \\
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$args \\
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-d results/ \\
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-n $prefix \\
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-p $task.cpus \\
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-i $seqs
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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seqsero2: \$( echo \$( SeqSero2_package.py --version 2>&1) | sed 's/^.*SeqSero2_package.py //' )
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END_VERSIONS
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"""
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}
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