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

nf-core/peddy @ 0.0.0-6c4ed3a

Manipulation, validation and exploration of pedigrees

pedigrees ped family

Latest version: 0.0.0-6c4ed3a

Total downloads: 5

Source: nf-core/modules

Authors: @rannick

Maintainers: @rannick

Manipulation, validation and exploration of pedigrees

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

include { PEDDY } from 'nf-core/peddy'

MIT License

Process

`Name`	`PEDDY`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`vcf` file	VCF file `*.vcf.gz`
`vcf_tbi` file	TBI file `*.vcf.gz.tbi`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`ped` file	PED/FAM file `*.{ped,fam}`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`sites` file	sites file. By defaults peddy uses hg19/GRCh37, "--sites hg38" can be specified in the process argument or a custom file following syntax https://github.com/brentp/peddy/blob/master/peddy/GRCH37.sites can be provided `*.sites`

Output 11 channels

#1 ped tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.peddy.ped` file	Inferred PED file `*.peddy.ped`

#2 html tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.html` file	HTML report `*.html`

#3 vs_html tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.vs.html` file	HTML file comparison between reported and inferred sex `*.vs.html`

#4 het_check_csv tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.het_check.csv` file	CSV file containing heterozygosity check. Rate of het calls, allele-balance at het calls, mean and median depth, and a PCA projection onto thousand genomes. `*.het_check.csv`

#5 het_check_png tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.het_check.png` file	PNG file containing heterozygosity check. Rate of het calls, allele-balance at het calls, mean and median depth, and a PCA projection onto thousand genomes. `*.het_check.png`

#6 ped_check_csv tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.ped_check.csv` file	CSV file containing pedigree check between reported and inferred sex `*.het_check.csv`

#7 ped_check_png tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.ped_check.png` file	PNG file containing pedigree check between reported and inferred sex `*.het_check.png`

#8 sex_check_csv tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.sex_check.csv` file	CSV file with sex check performs a comparison between the sex reported in the ped file and that inferred from the genotypes on the non-PAR regions of the X chromosome. `*.sex_check.csv`

#9 sex_check_png tuple

`${prefix}.sex_check.png`
`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]