nf-core_modules/modules/expansionhunter/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process EXPANSIONHUNTER {
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::expansionhunter=4.0.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/expansionhunter:4.0.2--he785bd8_0"
} else {
container "quay.io/biocontainers/expansionhunter:4.0.2--he785bd8_0"
}
input:
tuple val(meta), path(bam), path(bai)
path fasta
path variant_catalog
output:
tuple val(meta), path("*.vcf"), emit: vcf
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def gender = (meta.gender == 'male' || meta.gender == 1 || meta.gender == 'XY') ? "male" : "female"
"""
ExpansionHunter \\
$options.args \\
--reads $bam \\
--output-prefix $prefix \\
--reference $fasta \\
--variant-catalog $variant_catalog \\
--sex $gender
echo \$(ExpansionHunter --version 2>&1) | sed 's/^.*ExpansionHunter //' > ${software}.version.txt
"""
}