mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
b012b349c1
* implement plink2 VCF import * fix yaml indentation Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
43 lines
1.4 KiB
Text
43 lines
1.4 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process PLINK2_VCF {
|
|
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::plink2=2.00a2.3" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1"
|
|
} else {
|
|
container "quay.io/biocontainers/plink2:2.00a2.3--h712d239_1"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(vcf)
|
|
|
|
output:
|
|
tuple val(meta), path("*.pgen"), emit: pgen
|
|
tuple val(meta), path("*.psam"), emit: psam
|
|
tuple val(meta), path("*.pvar"), emit: pvar
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
"""
|
|
plink2 \\
|
|
$options.args \\
|
|
--vcf $vcf \\
|
|
--out ${prefix}
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(plink2 --version 2>&1 | sed 's/^PLINK v//; s/ 64.*\$//' )
|
|
END_VERSIONS
|
|
"""
|
|
}
|