mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
123 lines
7.7 KiB
Text
123 lines
7.7 KiB
Text
process VCFTOOLS {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? "bioconda::vcftools=0.1.16" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/vcftools:0.1.16--he513fc3_4' :
|
|
'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
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
def args_list = args.tokenize()
|
|
|
|
def bed_arg = (args.contains('--bed')) ? "--bed ${bed}" :
|
|
(args.contains('--exclude-bed')) ? "--exclude-bed ${bed}" :
|
|
(args.contains('--hapcount')) ? "--hapcount ${bed}" : ''
|
|
args_list.removeIf { it.contains('--bed') }
|
|
args_list.removeIf { it.contains('--exclude-bed') }
|
|
args_list.removeIf { it.contains('--hapcount') }
|
|
|
|
def diff_variant_arg = (args.contains('--diff')) ? "--diff ${diff_variant_file}" :
|
|
(args.contains('--gzdiff')) ? "--gzdiff ${diff_variant_file}" :
|
|
(args.contains('--diff-bcf')) ? "--diff-bcf ${diff_variant_file}" : ''
|
|
args_list.removeIf { it.contains('--diff') }
|
|
args_list.removeIf { it.contains('--gzdiff') }
|
|
args_list.removeIf { it.contains('--diff-bcf') }
|
|
|
|
def input_file = ("$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_list.join(' ')} \\
|
|
$bed_arg \\
|
|
$diff_variant_arg
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
vcftools: \$(echo \$(vcftools --version 2>&1) | sed 's/^.*VCFtools (//;s/).*//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|