mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
c5634ba99b
* initial commit [ci skip] * add stubs [ci skip] * Finalize the bcftools/view module * accomodate optional files * add optional region file * refer the targets file in the tests * all tests passing * documen the optional parameters
51 lines
1.7 KiB
Text
51 lines
1.7 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process BCFTOOLS_VIEW {
|
|
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::bcftools=1.13" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
|
|
} else {
|
|
container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(vcf), path(index)
|
|
path(regions)
|
|
path(targets)
|
|
path(samples)
|
|
|
|
output:
|
|
tuple val(meta), path("*.gz") , emit: vcf
|
|
path "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
def regions_file = regions ? "--regions-file ${regions}" : ""
|
|
def targets_file = targets ? "--targets-file ${targets}" : ""
|
|
def samples_file = samples ? "--samples-file ${samples}" : ""
|
|
|
|
|
|
"""
|
|
bcftools view \\
|
|
--output ${prefix}.vcf.gz \\
|
|
${regions_file} \\
|
|
${targets_file} \\
|
|
${samples_file} \\
|
|
$options.args \\
|
|
--threads $task.cpus \\
|
|
${vcf}
|
|
|
|
echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
|
|
"""
|
|
}
|