nf-core_modules/modules/glnexus/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process GLNEXUS {
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::glnexus=1.4.1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/glnexus:1.4.1--h40d77a6_0"
} else {
container "quay.io/biocontainers/glnexus:1.4.1--h40d77a6_0"
}
input:
tuple val(meta), path(gvcfs)
output:
tuple val(meta), path("*.bcf"), emit: bcf
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
// Make list of GVCFs to merge
def input = gvcfs.collect { it.toString() }
def avail_mem = 3
if (!task.memory) {
log.info '[Glnexus] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
glnexus_cli \\
--threads $task.cpus \\
--mem-gbytes $avail_mem \\
$options.args \\
${input.join(' ')} \\
> ${prefix}.bcf
echo \$(glnexus_cli 2>&1) | head -n 1 | sed 's/^.*release //; s/ .*\$//' > ${software}.version.txt
"""
}