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40 lines
1.2 KiB
Text
40 lines
1.2 KiB
Text
process SEXDETERRMINE {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::sexdeterrmine=1.1.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/sexdeterrmine:1.1.2--hdfd78af_1':
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'quay.io/biocontainers/sexdeterrmine:1.1.2--hdfd78af_1' }"
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input:
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tuple val(meta), path(depth)
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path(sample_list_file)
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output:
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tuple val(meta), path("*.json"), emit: json
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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 sample_list = sample_list_file ? '-f ${sample_list_file}' : ''
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if ("$depth" == "${prefix}.tsv") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
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"""
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sexdeterrmine \\
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-I $depth \\
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$sample_list \\
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$args \\
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> ${prefix}.tsv
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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sexdeterrmine: \$(echo \$(sexdeterrmine --version 2>&1))
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END_VERSIONS
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"""
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}
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