mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +00:00
906577873b
* New functions.nf * Convert code to create versions.yml * Update meta.yml * update output channel * Fix more meta.yml * Manually update remaining modules * remove superflous echo * Fix misformatted meta.yml files * Fix yaml, was list instead of dict * fix version for bcftools Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
48 lines
1.7 KiB
Text
48 lines
1.7 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } 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 "versions.yml" , 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
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(ExpansionHunter --version 2>&1 | sed 's/^.*ExpansionHunter //')
|
|
END_VERSIONS
|
|
"""
|
|
}
|