nf-core_modules/modules/bcftools/view/main.nf
Abhinav Sharma c5634ba99b
Add bcftools/view module (#669)
* 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
2021-09-12 19:51:40 +02:00

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
"""
}