nf-core_modules/modules/bcftools/roh/main.nf

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process BCFTOOLS_ROH {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0':
'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }"
input:
tuple val(meta), path(vcf), path(tbi)
path af_file
path genetic_map
path regions_file
path samples_file
path targets_file
output:
tuple val(meta), path("*.roh"), emit: roh
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 af_read = af_file ? "--AF-file ${af_file}" : ''
def gen_map = genetic_map ? "--genetic-map ${genetic_map}" : ''
def reg_file = regions_file ? "--regions-file ${regions_file}" : ''
def samp_file = samples_file ? "--samples-file ${samples_file}" : ''
def targ_file = targets_file ? "--targets-file ${targets_file}" : ''
"""
bcftools \\
roh \\
$args \\
$af_read \\
$gen_map \\
$reg_file \\
$samp_file \\
$targ_file \\
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-o ${prefix}.roh \\
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$vcf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.roh
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
}