// Import generic module functions include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) process PLINK_EXTRACT { 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::plink=1.90b6.21" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1" } else { container "quay.io/biocontainers/plink:1.90b6.21--h779adbc_1" } input: tuple val(meta), path(bed), path(bim), path(fam), path(variants) output: tuple val(meta), path("*.bed"), emit: bed tuple val(meta), path("*.bim"), emit: bim tuple val(meta), path("*.fam"), emit: fam path "versions.yml" , emit: versions script: def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" if( "$bed" == "${prefix}.bed" ) error "Input and output names are the same, use the suffix option to disambiguate" """ plink \\ --bfile ${meta.id} \\ $options.args \\ --extract $variants \\ --threads $task.cpus \\ --make-bed \\ --out $prefix cat <<-END_VERSIONS > versions.yml ${getProcessName(task.process)}: ${getSoftwareName(task.process)}: \$(echo \$(plink --version) | sed 's/^PLINK v//;s/64.*//') END_VERSIONS """ }