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

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

Produce pruned set of variants in approximatelinkage equilibrium

plink2 linkage equilibrium pruning

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @tdkaliki

Maintainers: @tdkaliki

Produce pruned set of variants in approximatelinkage equilibrium

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

include { PLINK2_INDEPPAIRWISE } from 'nf-core/plink2/indeppairwise'

MIT License

Process

`Name`	`PLINK2_INDEPPAIRWISE`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`plink_genotype_file` file	PLINK binary genotype table file or PLINK 2 binary genotype table file `*.{bed,pgen}`
`plink_variant_file` file	PLINK extended MAP file or PLINK 2 variant information file `*.{bim,pvar}`
`plink_sample_file` file	PLINK sample information file or PLINK 2 sample information file `*.{fam,psam}`

`win` integer	Window size in variant count or kilobase (if the 'kb' modifier is present) units, a variant count to shift the window at the end of each step, and a variance inflation factor (VIF) threshold. `*.{}`

`step` integer	Variant count to shift the window at the end of each step. `*.{}`

`r2` float	R squared threshold `*.{}`

Output 3 channels

#1 prune_in tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.prune.in` file	Variants in linkage equilibrium `*.prune.in`

#2 versions

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

#3 prune_out tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.prune.out` file	Excluded variants `*.prune.out`

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 19:04:30 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fplink2%2Findeppairwise/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/plink2/indeppairwise/blobs/sha256:968e5ece7187934f776f827f9178e49957d9b8252a34f516083100c102436ceb
Size	2.9 KB
Checksum	sha256:968e5ece7187934f776f827f9178e49957d9b8252a34f516083100c102436ceb
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:04:30 (UTC)		1	2.9 KB	-