nf-core_modules/modules/plink/vcf/main.nf
Davi Marcon 59ca7444cf
Adding plink/vcf module (#656)
* 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>
2021-09-14 08:51:40 +02:00

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
"""
}