nf-core_modules/modules/plink/extract/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process PLINK_EXTRACT {
tag "$meta.id"
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1"
} else {
container "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
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
if( "$bed" == "${prefix}.bed" ) error "Input and output names are the same, use the suffix option to disambiguate"
"""
plink \\
--bfile ${meta.id} \\
$options.args \\
--extract $variants \\
--threads $task.cpus \\
--make-bed \\
--out $prefix
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(plink --version) | sed 's/^PLINK v//;s/64.*//')
END_VERSIONS
"""
}