Nextflow Registry | nf-core/vcftools@0.0.0-6c4ed3a

nf-core/vcftools @ 0.0.0-6c4ed3a

A set of tools written in Perl and C++ for working with VCF files

VCFtools VCF sort

Latest version: 0.0.0-6c4ed3a

Total downloads: 12

Source: nf-core/modules

Authors: @Mark-S-Hill

Maintainers: @Mark-S-Hill

A set of tools written in Perl and C++ for working with VCF files

Add the following snippet to your workflow script to include this module.

include { VCFTOOLS } from 'nf-core/vcftools'

MIT License

Process

`Name`	`VCFTOOLS`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`variant_file` file	variant input file which can be vcf, vcf.gz, or bcf format.

`bed` file	bed file which can be used with different arguments in vcftools (optional)

`diff_variant_file` file	secondary variant file which can be used with the 'diff' suite of tools (optional)

Output 63 channels

#1 bcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bcf` file	bcf file (optional) `*.bcf`

#2 frq tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.frq` file	Allele frequency for each site (optional) `*.frq`

#3 hwe tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.hwe` file	Contains the Observed numbers of Homozygotes and Heterozygotes and the corresponding Expected numbers under HWE (optional) `*.hwe`

#4 ped tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.ped` file	output the genotype data in PLINK PED format (optional) `*.ped`

#5 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.vcf` file	vcf file (optional) `*.vcf`

#6 info tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.INFO` file	Extracted information from the INFO field in the VCF file (optional) `*.INFO`

#7 lroh tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.LROH` file	Long Runs of Homozygosity (optional) `*.LROH`

#8 map_ tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.map` file	output the genotype data in PLINK PED format (optional) `*.map`

#9 tfam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.tfam` file	output the genotype data in PLINK PED format (optional) `*.tfam`

#10 tped tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.tped` file	output the genotype data in PLINK PED format (optional) `*.tped`

#11 tstv tuple

`*.TsTv` file
`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]