nf-core_modules/modules/bcftools/norm/main.nf
2022-02-04 09:53:32 +01:00

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process BCFTOOLS_NORM {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input:
tuple val(meta), path(vcf)
path(fasta)
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}"
"""
bcftools norm \\
--fasta-ref ${fasta} \\
--output ${prefix}.vcf.gz \\
$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
"""
}