nf-core_modules/modules/vcfanno/main.nf

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process VCFANNO {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::vcfanno=0.3.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/vcfanno:0.3.3--h9ee0642_0':
'quay.io/biocontainers/vcfanno:0.3.3--h9ee0642_0' }"
input:
tuple val(meta), path(vcf), path(tbi)
path vcfanno_config
output:
tuple val(meta), path("*.vcf"), emit: vcf
path "versions.yml" , emit: versions
2022-02-04 08:53:32 +00:00
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
vcfanno \\
-p $task.cpus \\
$args \\
$vcfanno_config \\
$vcf \\
> ${prefix}_annotated.vcf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
vcfanno: \$(echo \$(vcfanno 2>&1 | grep version | cut -f3 -d' ' ))
END_VERSIONS
"""
}