Nextflow Registry | nf-core/plink2/extract@0.0.0-0c7146d

nf-core/plink2/extract @ 0.0.0-0c7146d

Subset plink pfiles with a text file of variant identifiers

plink2 extract identifiers

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @nebfield

Maintainers: @nebfield

Subset plink pfiles with a text file of variant identifiers

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

include { PLINK2_EXTRACT } from 'nf-core/plink2/extract'

MIT License

Process

`Name`	`PLINK2_EXTRACT`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`pgen` file	PLINK 2 binary genotype table `*.{pgen}`
`psam` file	PLINK 2 sample information file `*.{psam}`
`pvar` file	PLINK 2 variant information file `*.{pvar}`
`variants` file	A text file containing variant identifiers to keep (one per line) `*.{keep}`

Output 4 channels

#1 versions

`versions.yml` file	File containing software versions `versions.yml`

#2 extract_pgen tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.pgen` file	PLINK 2 binary genotype table, containing extracted variants `*.{pgen}`

#3 extract_psam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.psam` file	PLINK 2 sample information file associated with the extracted data `*.{psam}`

#4 extract_pvar tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.pvar.zst` file	PLINK 2 variant information file, containing extracted variants `*.{pvar.zst}`

Tool	Description	Homepage
plink2	Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner	http://www.cog-genomics.org/plink/2.0/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:04:25 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fplink2%2Fextract/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/plink2/extract/blobs/sha256:fd8a831039e1dd9f17b102ce22c84915091348958d0f2603d0583e8fef164b28
Size	2.9 KB
Checksum	sha256:fd8a831039e1dd9f17b102ce22c84915091348958d0f2603d0583e8fef164b28
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:04:25 (UTC)		1	2.9 KB	-