mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
42 lines
1.2 KiB
Text
42 lines
1.2 KiB
Text
process BCFTOOLS_REHEADER {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
|
|
container "${ 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 fai
|
|
path header
|
|
|
|
output:
|
|
tuple val(meta), path("*.vcf.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}"
|
|
def update_sequences = fai ? "-f $fai" : ""
|
|
def new_header = header ? "-h $header" : ""
|
|
"""
|
|
bcftools \\
|
|
reheader \\
|
|
$update_sequences \\
|
|
$new_header \\
|
|
$args \\
|
|
--threads $task.cpus \\
|
|
-o ${prefix}.vcf.gz \\
|
|
$vcf
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|