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