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

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process BCFTOOLS_INDEX {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
input:
tuple val(meta), path(vcf)
output:
tuple val(meta), path("*.csi"), optional:true, emit: csi
tuple val(meta), path("*.tbi"), optional:true, emit: tbi
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
bcftools \\
index \\
$args \\
--threads $task.cpus \\
$vcf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
}