mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
45 lines
1.3 KiB
Text
45 lines
1.3 KiB
Text
process GLNEXUS {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? "bioconda::glnexus=1.4.1" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/glnexus:1.4.1--h40d77a6_0' :
|
|
'quay.io/biocontainers/glnexus:1.4.1--h40d77a6_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(gvcfs)
|
|
|
|
output:
|
|
tuple val(meta), path("*.bcf"), emit: bcf
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${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 \\
|
|
$args \\
|
|
${input.join(' ')} \\
|
|
> ${prefix}.bcf
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
glnexus: \$( echo \$(glnexus_cli 2>&1) | head -n 1 | sed 's/^.*release v//; s/ .*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|