nf-core_modules/modules/bcftools/stats/main.nf
SusiJo 535975eb81
Update bcftools/stats for WES (#1893)
update bcftools/stats
2022-07-15 20:55:59 +02:00

36 lines
1.1 KiB
Text

process BCFTOOLS_STATS {
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(target_bed)
output:
tuple val(meta), path("*stats.txt"), emit: stats
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 target = target_bed ? "--regions-file ${target_bed}" : ""
"""
bcftools stats \\
$args \\
$target \\
$vcf > ${prefix}.bcftools_stats.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
}