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53 lines
1.5 KiB
Text
53 lines
1.5 KiB
Text
process GENMOD_MODELS {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::genmod=3.7.4 conda-forge::python=3.4.5" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/genmod:3.7.4--pyh5e36f6f_0':
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'quay.io/biocontainers/genmod:3.7.4--pyh5e36f6f_0' }"
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input:
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tuple val(meta), path(input_vcf)
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path (fam)
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path (reduced_penetrance)
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output:
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tuple val(meta), path("*_models.vcf"), emit: vcf
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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 family_file = fam ? "--family_file ${fam}" : ""
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def pen_file = reduced_penetrance ? "--reduced_penetrance ${reduced_penetrance}" : ""
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"""
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genmod \\
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models \\
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$args \\
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$pen_file \\
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$family_file \\
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--processes ${task.cpus} \\
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--outfile ${prefix}_models.vcf \\
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$input_vcf
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' ))
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}_models.vcf
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' ))
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END_VERSIONS
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"""
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}
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