mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
59ca7444cf
* adding plink module using nf-core tool [ci skip] * Restructures the project for plink/vcf (#1) * Add version string for plink * Create a plink/vcf module * small tweaks on main.nf and started to test [ci skip] * small changes on test args, local test with docker passed! * Update plink/vcf module listing * Update tag * fix tags as per linting guidelines * revert to the original state of tags * adding --threads to `main.nf` and `meta.yml` information Co-authored-by: Abhinav Sharma <abhi18av@users.noreply.github.com>
44 lines
1.5 KiB
Text
44 lines
1.5 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process PLINK_VCF {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
publishDir "${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(vcf)
|
|
|
|
output:
|
|
tuple val(meta), path("*.bed"), emit: bed, optional: true
|
|
tuple val(meta), path("*.bim"), emit: bim, optional: true
|
|
tuple val(meta), path("*.fam"), emit: fam, optional: true
|
|
|
|
path "*.version.txt", emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
|
|
"""
|
|
plink \\
|
|
--vcf ${vcf} \\
|
|
$options.args \\
|
|
--threads $task.cpus \\
|
|
--out ${prefix}
|
|
|
|
echo \$(plink --version 2>&1) | sed 's/^PLINK //' | sed 's/..-bit.*//'> ${software}.version.txt
|
|
"""
|
|
}
|