mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
40 lines
1.3 KiB
Text
40 lines
1.3 KiB
Text
process PLINK_EXTRACT {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1' :
|
|
'quay.io/biocontainers/plink:1.90b6.21--h779adbc_1' }"
|
|
|
|
input:
|
|
tuple val(meta), path(bed), path(bim), path(fam), path(variants)
|
|
|
|
output:
|
|
tuple val(meta), path("*.bed"), emit: bed
|
|
tuple val(meta), path("*.bim"), emit: bim
|
|
tuple val(meta), path("*.fam"), emit: fam
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
if( "$bed" == "${prefix}.bed" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
|
|
"""
|
|
plink \\
|
|
--bfile ${meta.id} \\
|
|
$args \\
|
|
--extract $variants \\
|
|
--threads $task.cpus \\
|
|
--make-bed \\
|
|
--out $prefix
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
plink: \$(echo \$(plink --version) | sed 's/^PLINK v//;s/64.*//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|