nf-core_modules/modules/vcftools/main.nf
Harshil Patel cf15ece503
Address Jose's comments in #780 (#781)
* Remove def software line

* Replace version with versions in emit statement

* Fix default software names

* Address Jose's comments in #780
2021-10-01 15:54:50 +02:00

130 lines
8.2 KiB
Text

// 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:
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
path "versions.yml" , emit: versions
script:
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)}: \$(echo \$(vcftools --version 2>&1) | sed 's/^.*VCFtools (//;s/).*//')
END_VERSIONS
"""
}