process PLINK2_VCF { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' : 'quay.io/biocontainers/plink2:2.00a2.3--h712d239_1' }" input: tuple val(meta), path(vcf) output: tuple val(meta), path("*.pgen") , emit: pgen tuple val(meta), path("*.psam") , emit: psam tuple val(meta), path("*.pvar.zst"), emit: pvar 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}" def mem_mb = task.memory.toMega() """ plink2 \\ --threads $task.cpus \\ --memory $mem_mb \\ $args \\ --vcf $vcf \\ --make-pgen vzs \\ --out ${prefix} cat <<-END_VERSIONS > versions.yml "${task.process}": plink2: \$(plink2 --version 2>&1 | sed 's/^PLINK v//; s/ 64.*\$//' ) END_VERSIONS """ }