mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
42 lines
1.4 KiB
Text
42 lines
1.4 KiB
Text
process PLINK2_EXTRACT {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' :
|
|
'quay.io/biocontainers/plink2:2.00a2.3--h712d239_1' }"
|
|
|
|
input:
|
|
tuple val(meta), path(pgen), path(psam), path(pvar), path(variants)
|
|
|
|
output:
|
|
tuple val(meta), path("*.pgen") , emit: extract_pgen
|
|
tuple val(meta), path("*.psam") , emit: extract_psam
|
|
tuple val(meta), path("*.pvar.zst"), emit: extract_pvar
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
if( "$pgen" == "${prefix}.pgen" ) error "Input and output names are the same, use \"task.ext.prefix\" in modules.config to disambiguate!"
|
|
def mem_mb = task.memory.toMega()
|
|
"""
|
|
plink2 \\
|
|
--threads $task.cpus \\
|
|
--memory $mem_mb \\
|
|
--pfile ${pgen.baseName} \\
|
|
$args \\
|
|
--extract $variants \\
|
|
--make-pgen vzs \\
|
|
--out ${prefix}
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
plink2: \$(plink2 --version 2>&1 | sed 's/^PLINK v//; s/ 64.*\$//' )
|
|
END_VERSIONS
|
|
"""
|
|
}
|