nf-core_modules/modules/stranger/main.nf

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process STRANGER {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::stranger=0.8.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/stranger:0.8.1--pyh5e36f6f_0':
'quay.io/biocontainers/stranger:0.8.1--pyh5e36f6f_0' }"
input:
tuple val(meta), path(vcf)
path variant_catalog
output:
tuple val(meta), path("*.gz"), emit: vcf
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}"
def options_variant_catalog = variant_catalog ? "--repeats-file $variant_catalog" : ""
"""
stranger \\
$args \\
$vcf \\
$options_variant_catalog | gzip --no-name > ${prefix}.vcf.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
stranger: \$( stranger --version )
END_VERSIONS
"""
}