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34 lines
1,005 B
Text
34 lines
1,005 B
Text
process SVDB_QUERY {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::svdb=2.5.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/svdb:2.5.0--py39hcbe4a3b_0':
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'quay.io/biocontainers/svdb:2.5.0--py39hcbe4a3b_0' }"
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input:
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tuple val(meta), path(vcf)
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path (vcf_db)
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output:
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tuple val(meta), path("*_ann_svdbq.vcf"), emit: vcf
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path "versions.yml" , emit: versions
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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svdb \\
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--query \\
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$args \\
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--db $vcf_db \\
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--query_vcf $vcf \\
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>${prefix}_ann_svdbq.vcf
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
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END_VERSIONS
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"""
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}
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