nf-core_modules/modules/vcf2db/main.nf

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process VCF2DB {
tag "$meta.id"
label 'process_medium'
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// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
conda (params.enable_conda ? "bioconda::vcf2db=2020.02.24" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/vcf2db:2020.02.24--hdfd78af_1':
'quay.io/biocontainers/vcf2db:2020.02.24--hdfd78af_1' }"
input:
tuple val(meta), path(vcf), path(ped)
output:
tuple val(meta), path("*.db") , emit: db
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
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def VERSION = "2020.02.24" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
vcf2db.py \\
$vcf \\
$ped \\
${prefix}.db \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
vcf2db: $VERSION
END_VERSIONS
"""
}