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 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 """ }