Nextflow Registry | nf-core/plink/extract@0.0.0-0c7146d

nf-core/plink/extract @ 0.0.0-0c7146d

Subset plink bfiles with a text file of variant identifiers

extract plink subset bfiles

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @nebfield

Maintainers: @nebfield

Subset plink bfiles with a text file of variant identifiers

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

include { PLINK_EXTRACT } from 'nf-core/plink/extract'

MIT License

Process

`Name`	`PLINK_EXTRACT`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bed` file	PLINK binary biallelic genotype table `*.{bed}`
`bim` file	PLINK extended MAP file `*.{bim}`
`fam` file	PLINK sample information file `*.{fam}`
`variants` file	A text file containing variant identifiers to keep (one per line) `*.{keep}`

Output 4 channels

#1 bed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bed` file	PLINK binary biallelic genotype table `*.{bed}`

#2 bim tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bim` file	PLINK extended MAP file `*.{bim}`

#3 fam tuple

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

#4 versions_plink tuple

`${task.process}` string	The name of the process
`plink` string	The name of the tool
`plink --version 2>&1 \| sed 's/^PLINK v//;s/ .*//'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
plink	Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.	https://www.cog-genomics.org/plink

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:03:38 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fplink%2Fextract/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/plink/extract/blobs/sha256:01414de7d64967416e551404ffb0dbc58985fda01ec5ed6db7ded0f9be0f9f24
Size	3.0 KB
Checksum	sha256:01414de7d64967416e551404ffb0dbc58985fda01ec5ed6db7ded0f9be0f9f24
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:03:38 (UTC)		1	3.0 KB	-