// Import generic module functions include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) process VCFTOOLS { 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::vcftools=0.1.16" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://depot.galaxyproject.org/singularity/vcftools:0.1.16--he513fc3_4" } else { container "quay.io/biocontainers/vcftools:0.1.16--he513fc3_4" } input: // Owing to the nature of vcftools we here provide solutions to working with optional bed files and optional // alternative variant files, for use with the 'diff' suite of tools. // Other optional input files can be utilised in a similar way to below but we do not exhaustively itterate through all // possible options. Instead we leave that to the user. tuple val(meta), path(variant_file) path(bed) path(diff_variant_file) output: path("versions.yml") , emit: version tuple val(meta), path("*.vcf"), optional:true, emit: vcf tuple val(meta), path("*.bcf"), optional:true, emit: bcf tuple val(meta), path("*.frq"), optional:true, emit: frq tuple val(meta), path("*.frq.count"), optional:true, emit: frq_count tuple val(meta), path("*.idepth"), optional:true, emit: idepth tuple val(meta), path("*.ldepth"), optional:true, emit: ldepth tuple val(meta), path("*.ldepth.mean"), optional:true, emit: ldepth_mean tuple val(meta), path("*.gdepth"), optional:true, emit: gdepth tuple val(meta), path("*.hap.ld"), optional:true, emit: hap_ld tuple val(meta), path("*.geno.ld"), optional:true, emit: geno_ld tuple val(meta), path("*.geno.chisq"), optional:true, emit: geno_chisq tuple val(meta), path("*.list.hap.ld"), optional:true, emit: list_hap_ld tuple val(meta), path("*.list.geno.ld"), optional:true, emit: list_geno_ld tuple val(meta), path("*.interchrom.hap.ld"), optional:true, emit: interchrom_hap_ld tuple val(meta), path("*.interchrom.geno.ld"), optional:true, emit: interchrom_geno_ld tuple val(meta), path("*.TsTv"), optional:true, emit: tstv tuple val(meta), path("*.TsTv.summary"), optional:true, emit: tstv_summary tuple val(meta), path("*.TsTv.count"), optional:true, emit: tstv_count tuple val(meta), path("*.TsTv.qual"), optional:true, emit: tstv_qual tuple val(meta), path("*.FILTER.summary"), optional:true, emit: filter_summary tuple val(meta), path("*.sites.pi"), optional:true, emit: sites_pi tuple val(meta), path("*.windowed.pi"), optional:true, emit: windowed_pi tuple val(meta), path("*.weir.fst"), optional:true, emit: weir_fst tuple val(meta), path("*.het"), optional:true, emit: heterozygosity tuple val(meta), path("*.hwe"), optional:true, emit: hwe tuple val(meta), path("*.Tajima.D"), optional:true, emit: tajima_d tuple val(meta), path("*.ifreqburden"), optional:true, emit: freq_burden tuple val(meta), path("*.LROH"), optional:true, emit: lroh tuple val(meta), path("*.relatedness"), optional:true, emit: relatedness tuple val(meta), path("*.relatedness2"), optional:true, emit: relatedness2 tuple val(meta), path("*.lqual"), optional:true, emit: lqual tuple val(meta), path("*.imiss"), optional:true, emit: missing_individual tuple val(meta), path("*.lmiss"), optional:true, emit: missing_site tuple val(meta), path("*.snpden"), optional:true, emit: snp_density tuple val(meta), path("*.kept.sites"), optional:true, emit: kept_sites tuple val(meta), path("*.removed.sites"), optional:true, emit: removed_sites tuple val(meta), path("*.singletons"), optional:true, emit: singeltons tuple val(meta), path("*.indel.hist"), optional:true, emit: indel_hist tuple val(meta), path("*.hapcount"), optional:true, emit: hapcount tuple val(meta), path("*.mendel"), optional:true, emit: mendel tuple val(meta), path("*.FORMAT"), optional:true, emit: format tuple val(meta), path("*.INFO"), optional:true, emit: info tuple val(meta), path("*.012"), optional:true, emit: genotypes_matrix tuple val(meta), path("*.012.indv"), optional:true, emit: genotypes_matrix_individual tuple val(meta), path("*.012.pos"), optional:true, emit: genotypes_matrix_position tuple val(meta), path("*.impute.hap"), optional:true, emit: impute_hap tuple val(meta), path("*.impute.hap.legend"), optional:true, emit: impute_hap_legend tuple val(meta), path("*.impute.hap.indv"), optional:true, emit: impute_hap_indv tuple val(meta), path("*.ldhat.sites"), optional:true, emit: ldhat_sites tuple val(meta), path("*.ldhat.locs"), optional:true, emit: ldhat_locs tuple val(meta), path("*.BEAGLE.GL"), optional:true, emit: beagle_gl tuple val(meta), path("*.BEAGLE.PL"), optional:true, emit: beagle_pl tuple val(meta), path("*.ped"), optional:true, emit: ped tuple val(meta), path("*.map"), optional:true, emit: map_ tuple val(meta), path("*.tped"), optional:true, emit: tped tuple val(meta), path("*.tfam"), optional:true, emit: tfam tuple val(meta), path("*.diff.sites_in_files"), optional:true, emit: diff_sites_in_files tuple val(meta), path("*.diff.indv_in_files"), optional:true, emit: diff_indv_in_files tuple val(meta), path("*.diff.sites"), optional:true, emit: diff_sites tuple val(meta), path("*.diff.indv"), optional:true, emit: diff_indv tuple val(meta), path("*.diff.discordance.matrix"), optional:true, emit: diff_discd_matrix tuple val(meta), path("*.diff.switch"), optional:true, emit: diff_switch_error script: def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def args = options.args.tokenize() def bed_arg = (options.args.contains('--bed')) ? "--bed ${bed}" : (options.args.contains('--exclude-bed')) ? "--exclude-bed ${bed}" : (options.args.contains('--hapcount')) ? "--hapcount ${bed}" : '' args.removeIf { it.contains('--bed') } args.removeIf { it.contains('--exclude-bed') } args.removeIf { it.contains('--hapcount') } def diff_variant_arg = (options.args.contains('--diff')) ? "--diff ${diff_variant_file}" : (options.args.contains('--gzdiff')) ? "--gzdiff ${diff_variant_file}" : (options.args.contains('--diff-bcf')) ? "--diff-bcf ${diff_variant_file}" : '' args.removeIf { it.contains('--diff') } args.removeIf { it.contains('--gzdiff') } args.removeIf { it.contains('--diff-bcf') } def input_file = ("$variant_file".endsWith(".vcf")) ? "--vcf ${variant_file}" : ("$variant_file".endsWith(".vcf.gz")) ? "--gzvcf ${variant_file}" : ("$variant_file".endsWith(".bcf")) ? "--bcf ${variant_file}" : '' """ vcftools \\ $input_file \\ --out $prefix \\ ${args.join(' ')} \\ $bed_arg \\ $diff_variant_arg \\ cat <<-END_VERSIONS > versions.yml ${getProcessName(task.process)}: ${getSoftwareName(task.process)}: \$(vcftools --version 2>&1 | sed 's/^.*vcftools //; s/Using.*\$//') END_VERSIONS """ }