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https://github.com/MillironX/nf-core_modules.git
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add vcftools module (#334)
* add vcftools module * fix padding issue * fix linting errors
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61
software/vcftools/functions.nf
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61
software/vcftools/functions.nf
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/*
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* -----------------------------------------------------
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* Utility functions used in nf-core DSL2 module files
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* -----------------------------------------------------
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*/
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/*
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* Extract name of software tool from process name using $task.process
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*/
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def getSoftwareName(task_process) {
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return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
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}
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/*
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* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
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*/
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def initOptions(Map args) {
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def Map options = [:]
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options.args = args.args ?: ''
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options.args2 = args.args2 ?: ''
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options.args3 = args.args3 ?: ''
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options.publish_by_id = args.publish_by_id ?: false
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options.publish_dir = args.publish_dir ?: ''
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options.publish_files = args.publish_files
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options.suffix = args.suffix ?: ''
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return options
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}
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/*
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* Tidy up and join elements of a list to return a path string
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*/
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def getPathFromList(path_list) {
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def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
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paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
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return paths.join('/')
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}
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/*
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* Function to save/publish module results
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*/
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def saveFiles(Map args) {
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if (!args.filename.endsWith('.version.txt')) {
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def ioptions = initOptions(args.options)
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def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
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if (ioptions.publish_by_id) {
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path_list.add(args.publish_id)
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}
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if (ioptions.publish_files instanceof Map) {
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for (ext in ioptions.publish_files) {
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if (args.filename.endsWith(ext.key)) {
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def ext_list = path_list.collect()
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ext_list.add(ext.value)
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return "${getPathFromList(ext_list)}/$args.filename"
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}
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}
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} else if (ioptions.publish_files == null) {
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return "${getPathFromList(path_list)}/$args.filename"
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}
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}
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}
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129
software/vcftools/main.nf
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129
software/vcftools/main.nf
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process VCFTOOLS {
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tag "$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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294
software/vcftools/meta.yml
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294
software/vcftools/meta.yml
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name: vcftools
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description: A set of tools written in Perl and C++ for working with VCF files
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keywords: VCF
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- sort
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tools:
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- vcftools:
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description: A set of tools written in Perl and C++ for working with VCF files. This package only contains the C++ libraries whereas the package perl-vcftools-vcf contains the perl libraries
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homepage: http://vcftools.sourceforge.net/
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documentation: http://vcftools.sourceforge.net/man_latest.html
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tool_dev_url: None
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doi:
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licence: ['LGPL']
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- variant_file:
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type: file
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description: variant input file which can be vcf, vcf.gz, or bcf format.
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- bed:
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type: file
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description: bed file which can be used with different arguments in vcftools (optional)
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- diff_variant_file:
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type: file
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description: secondary variant file which can be used with the 'diff' suite of tools (optional)
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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- vcf:
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type: file
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description: vcf file (optional)
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pattern: "*.vcf"
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- bcf:
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type: file
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description: bcf file (optional)
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pattern: "*.bcf"
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- frq:
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type: file
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description: Allele frequency for each site (optional)
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pattern: "*.frq"
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- frq_count:
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type: file
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description: Allele counts for each site (optional)
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pattern: "*.frq.count"
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- idepth:
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type: file
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description: mean depth per individual (optional)
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pattern: "*.idepth"
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- ldepth:
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type: file
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description: depth per site summed across individuals (optional)
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pattern: "*.ildepth"
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- ldepth_mean:
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type: file
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description: mean depth per site calculated across individuals (optional)
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pattern: "*.ldepth.mean"
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- gdepth:
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type: file
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description: depth for each genotype in vcf file (optional)
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pattern: "*.gdepth"
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- hap_ld:
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type: file
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description: r2, D, and D’ statistics using phased haplotypes (optional)
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pattern: "*.hap.ld"
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- geno_ld:
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type: file
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description: squared correlation coefficient between genotypes encoded as 0, 1 and 2 to represent the number of non-reference alleles in each individual (optional)
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pattern: "*.geno.ld"
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- geno_chisq:
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type: file
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description: test for genotype independence via the chi-squared statistic (optional)
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pattern: "*.geno.chisq"
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- list_hap_ld:
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type: file
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description: r2 statistics of the sites contained in the provided input file verses all other sites (optional)
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pattern: "*.list.hap.ld"
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- list_geno_ld:
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type: file
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description: r2 statistics of the sites contained in the provided input file verses all other sites (optional)
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pattern: "*.list.geno.ld"
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- interchrom_hap_ld:
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type: file
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description: r2 statistics for sites (haplotypes) on different chromosomes (optional)
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pattern: "*.interchrom.hap.ld"
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- interchrom_geno_ld:
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type: file
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description: r2 statistics for sites (genotypes) on different chromosomes (optional)
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pattern: "*.interchrom.geno.ld"
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- tstv:
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type: file
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description: Transition / Transversion ratio in bins of size defined in options (optional)
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pattern: "*.TsTv"
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- tstv_summary:
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type: file
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description: Summary of all Transitions and Transversions (optional)
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pattern: "*.TsTv.summary"
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- tstv_count:
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type: file
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description: Transition / Transversion ratio as a function of alternative allele count (optional)
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pattern: "*.TsTv.count"
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- tstv_qual:
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type: file
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description: Transition / Transversion ratio as a function of SNP quality threshold (optional)
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pattern: "*.TsTv.qual"
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- filter_summary:
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type: file
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description: Summary of the number of SNPs and Ts/Tv ratio for each FILTER category (optional)
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pattern: "*.FILTER.summary"
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- sites_pi:
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type: file
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description: Nucleotide divergency on a per-site basis (optional)
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pattern: "*.sites.pi"
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- windowed_pi:
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type: file
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description: Nucleotide diversity in windows, with window size determined by options (optional)
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pattern: "*windowed.pi"
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- weir_fst:
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type: file
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description: Fst estimate from Weir and Cockerham’s 1984 paper (optional)
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pattern: "*.weir.fst"
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- heterozygosity:
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type: file
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description: Heterozygosity on a per-individual basis (optional)
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pattern: "*.het"
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- hwe:
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type: file
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description: Contains the Observed numbers of Homozygotes and Heterozygotes and the corresponding Expected numbers under HWE (optional)
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pattern: "*.hwe"
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- tajima_d:
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type: file
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description: Tajima’s D statistic in bins with size of the specified number in options (optional)
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pattern: "*.Tajima.D"
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- freq_burden:
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type: file
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description: Number of variants within each individual of a specific frequency in options (optional)
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pattern: "*.ifreqburden"
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- lroh:
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type: file
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description: Long Runs of Homozygosity (optional)
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pattern: "*.LROH"
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- relatedness:
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type: file
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description: Relatedness statistic based on the method of Yang et al, Nature Genetics 2010 (doi:10.1038/ng.608) (optional)
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pattern: "*.relatedness"
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- relatedness2:
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type: file
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description: Relatedness statistic based on the method of Manichaikul et al., BIOINFORMATICS 2010 (doi:10.1093/bioinformatics/btq559) (optional)
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pattern: "*.relatedness2"
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- lqual:
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type: file
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description: per-site SNP quality (optional)
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pattern: "*.lqual"
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- missing_individual:
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type: file
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description: Missingness on a per-individual basis (optional)
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pattern: "*.imiss"
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- missing_site:
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type: file
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description: Missingness on a per-site basis (optional)
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pattern: "*.lmiss"
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- snp_density:
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type: file
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description: Number and density of SNPs in bins of size defined by option (optional)
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pattern: "*.snpden"
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- kept_sites:
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type: file
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description: All sites that have been kept after filtering (optional)
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pattern: "*.kept.sites"
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- removed_sites:
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type: file
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description: All sites that have been removed after filtering (optional)
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pattern: "*.removed.sites"
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- singeltons:
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type: file
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description: Location of singletons, and the individual they occur in (optional)
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pattern: "*.singeltons"
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- indel_hist:
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type: file
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description: Histogram file of the length of all indels (including SNPs) (optional)
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pattern: "*.indel_hist"
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- hapcount:
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type: file
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description: Unique haplotypes within user specified bins (optional)
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pattern: "*.hapcount"
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- mendel:
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type: file
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description: Mendel errors identified in trios (optional)
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pattern: "*.mendel"
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- format:
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type: file
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description: Extracted information from the genotype fields in the VCF file relating to a specfied FORMAT identifier (optional)
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pattern: "*.FORMAT"
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- info:
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type: file
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description: Extracted information from the INFO field in the VCF file (optional)
|
||||
pattern: "*.INFO"
|
||||
- genotypes_matrix:
|
||||
type: file
|
||||
description: |
|
||||
Genotypes output as large matrix.
|
||||
Genotypes of each individual on a separate line.
|
||||
Genotypes are represented as 0, 1 and 2, where the number represent that number of non-reference alleles.
|
||||
Missing genotypes are represented by -1 (optional)
|
||||
pattern: "*.012"
|
||||
- genotypes_matrix_individual:
|
||||
type: file
|
||||
description: Details the individuals included in the main genotypes_matrix file (optional)
|
||||
pattern: "*.012.indv"
|
||||
- genotypes_matrix_position:
|
||||
type: file
|
||||
description: Details the site locations included in the main genotypes_matrix file (optional)
|
||||
pattern: "*.012.pos"
|
||||
- impute_hap:
|
||||
type: file
|
||||
description: Phased haplotypes in IMPUTE reference-panel format (optional)
|
||||
pattern: "*.impute.hap"
|
||||
- impute_hap_legend:
|
||||
type: file
|
||||
description: Impute haplotype legend file (optional)
|
||||
pattern: "*.impute.hap.legend"
|
||||
- impute_hap_indv:
|
||||
type: file
|
||||
description: Impute haplotype individuals file (optional)
|
||||
pattern: "*.impute.hap.indv"
|
||||
- ldhat_sites:
|
||||
type: file
|
||||
description: Output data in LDhat format, sites (optional)
|
||||
pattern: "*.ldhat.sites"
|
||||
- ldhat_locs:
|
||||
type: file
|
||||
description: output data in LDhat format, locations (optional)
|
||||
pattern: "*.ldhat.locs"
|
||||
- beagle_gl:
|
||||
type: file
|
||||
description: Genotype likelihoods for biallelic sites (optional)
|
||||
pattern: "*.BEAGLE.GL"
|
||||
- beagle_pl:
|
||||
type: file
|
||||
description: Genotype likelihoods for biallelic sites (optional)
|
||||
pattern: "*.BEAGLE.PL"
|
||||
- ped:
|
||||
type: file
|
||||
description: output the genotype data in PLINK PED format (optional)
|
||||
pattern: "*.ped"
|
||||
- map_:
|
||||
type: file
|
||||
description: output the genotype data in PLINK PED format (optional)
|
||||
pattern: "*.map"
|
||||
- tped:
|
||||
type: file
|
||||
description: output the genotype data in PLINK PED format (optional)
|
||||
pattern: "*.tped"
|
||||
- tfam:
|
||||
type: file
|
||||
description: output the genotype data in PLINK PED format (optional)
|
||||
pattern: "*.tfam"
|
||||
- diff_sites_in_files:
|
||||
type: file
|
||||
description: Sites that are common / unique to each file specified in optional inputs (optional)
|
||||
pattern: "*.diff.sites.in.files"
|
||||
- diff_indv_in_files:
|
||||
type: file
|
||||
description: Individuals that are common / unique to each file specified in optional inputs (optional)
|
||||
pattern: "*.diff.indv.in.files"
|
||||
- diff_sites:
|
||||
type: file
|
||||
description: Discordance on a site by site basis, specified in optional inputs (optional)
|
||||
pattern: "*.diff.sites"
|
||||
- diff_indv:
|
||||
type: file
|
||||
description: Discordance on a individual by individual basis, specified in optional inputs (optional)
|
||||
pattern: "*.diff.indv"
|
||||
- diff_discd_matrix:
|
||||
type: file
|
||||
description: Discordance matrix between files specified in optional inputs (optional)
|
||||
pattern: "*.diff.discordance.matrix"
|
||||
- diff_switch_error:
|
||||
type: file
|
||||
description: Switch errors found between sites (optional)
|
||||
pattern: "*.diff.switch"
|
||||
|
||||
authors:
|
||||
- "@Mark-S-Hill"
|
|
@ -426,3 +426,7 @@ unicycler:
|
|||
untar:
|
||||
- software/untar/**
|
||||
- tests/software/untar/**
|
||||
|
||||
vcftools:
|
||||
- software/vcftools/**
|
||||
- tests/software/vcftools/**
|
||||
|
|
46
tests/software/vcftools/main.nf
Normal file
46
tests/software/vcftools/main.nf
Normal file
|
@ -0,0 +1,46 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { VCFTOOLS as VCFTOOLS_BASE} from '../../../software/vcftools/main.nf' addParams( options: ['args': '--freq'] )
|
||||
include { VCFTOOLS as VCFTOOLS_OPTIONAL} from '../../../software/vcftools/main.nf' addParams( options: ['args': '--freq --exclude-bed'] )
|
||||
|
||||
workflow test_vcftools_vcf_base {
|
||||
|
||||
def input = []
|
||||
input = [ [ id:'test' ], // meta map
|
||||
file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf", checkIfExists: true) ]
|
||||
|
||||
VCFTOOLS_BASE ( input, [], [] )
|
||||
}
|
||||
|
||||
workflow test_vcftools_vcfgz_base {
|
||||
|
||||
def input = []
|
||||
input = [ [ id:'test' ], // meta map
|
||||
file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf.gz", checkIfExists: true) ]
|
||||
|
||||
VCFTOOLS_BASE ( input, [], [] )
|
||||
}
|
||||
|
||||
workflow test_vcftools_vcf_optional {
|
||||
|
||||
def input = []
|
||||
def bed = file("${launchDir}/tests/data/genomics/sarscov2/bed/test.bed", checkIfExists: true)
|
||||
|
||||
input = [ [ id:'test' ], // meta map
|
||||
file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf", checkIfExists: true) ]
|
||||
|
||||
VCFTOOLS_OPTIONAL ( input, bed, [] )
|
||||
}
|
||||
|
||||
workflow test_vcftools_vcfgz_optional {
|
||||
|
||||
def input = []
|
||||
def bed = file("${launchDir}/tests/data/genomics/sarscov2/bed/test.bed", checkIfExists: true)
|
||||
|
||||
input = [ [ id:'test' ], // meta map
|
||||
file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf.gz", checkIfExists: true) ]
|
||||
|
||||
VCFTOOLS_OPTIONAL ( input, bed, [] )
|
||||
}
|
35
tests/software/vcftools/test.yml
Normal file
35
tests/software/vcftools/test.yml
Normal file
|
@ -0,0 +1,35 @@
|
|||
- name: vcftools test_vcftools_vcf_base
|
||||
command: nextflow run tests/software/vcftools -entry test_vcftools_vcf_base -c tests/config/nextflow.config
|
||||
tags:
|
||||
- vcftools
|
||||
- vcftools_vcf_base
|
||||
files:
|
||||
- path: output/vcftools/test.frq
|
||||
md5sum: 7f126655f17268fd1a338734f62868e9
|
||||
|
||||
- name: vcftools test_vcftools_vcfgz_base
|
||||
command: nextflow run tests/software/vcftools -entry test_vcftools_vcfgz_base -c tests/config/nextflow.config
|
||||
tags:
|
||||
- vcftools_vcfgz_base
|
||||
- vcftools
|
||||
files:
|
||||
- path: output/vcftools/test.frq
|
||||
md5sum: 7f126655f17268fd1a338734f62868e9
|
||||
|
||||
- name: vcftools test_vcftools_vcf_optional
|
||||
command: nextflow run tests/software/vcftools -entry test_vcftools_vcf_optional -c tests/config/nextflow.config
|
||||
tags:
|
||||
- vcftools
|
||||
- vcftools_vcf_optional
|
||||
files:
|
||||
- path: output/vcftools/test.frq
|
||||
md5sum: 7f126655f17268fd1a338734f62868e9
|
||||
|
||||
- name: vcftools test_vcftools_vcfgz_optional
|
||||
command: nextflow run tests/software/vcftools -entry test_vcftools_vcfgz_optional -c tests/config/nextflow.config
|
||||
tags:
|
||||
- vcftools
|
||||
- vcftools_vcfgz_optional
|
||||
files:
|
||||
- path: output/vcftools/test.frq
|
||||
md5sum: 7f126655f17268fd1a338734f62868e9
|
Loading…
Reference in a new issue