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https://github.com/MillironX/nf-core_modules.git
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46 lines
1.3 KiB
Text
46 lines
1.3 KiB
Text
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process SVTK_STANDARDIZE {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::svtk=0.0.20190615" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/svtk:0.0.20190615--py37h73a75cf_2':
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'quay.io/biocontainers/svtk:0.0.20190615--py37h73a75cf_2' }"
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input:
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tuple val(meta), path(vcf)
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path fasta_fai
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output:
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tuple val(meta), path("*.std.vcf.gz"), emit: standardized_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 arguments = args.args ?: ''
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def caller = args.caller ?: 'delly'
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def VERSION = '0.0.20190615' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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def contigs = fasta_fai ? "--contigs ${fasta_fai}" : ""
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"""
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svtk standardize \\
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${arguments} \\
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${contigs} \\
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${vcf} \\
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${prefix}.std.vcf.gz \\
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${caller}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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svtk: ${VERSION}
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END_VERSIONS
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"""
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}
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