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cf15ece503
* Remove def software line * Replace version with versions in emit statement * Fix default software names * Address Jose's comments in #780
130 lines
8.2 KiB
Text
130 lines
8.2 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } 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), meta:meta, publish_by_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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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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path "versions.yml" , emit: versions
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script:
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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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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(vcftools --version 2>&1) | sed 's/^.*VCFtools (//;s/).*//')
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END_VERSIONS
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"""
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}
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