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

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

Produce a pruned subset of markers that are in approximate linkage equilibrium with each other.

plink indep variant pruning bim fam

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @atrigila

Maintainers: @atrigila

Produce a pruned subset of markers that are in approximate linkage equilibrium with each other.

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

include { PLINK_INDEP } from 'nf-core/plink/indep'

MIT License

Process

`Name`	`PLINK_INDEP`

Input 4 channels

#1 tuple

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

`window_size` string	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.

`variant_count` string	Variant count to shift the window at the end of each step.

`variance_inflation_factor` string	Variance inflation factor (VIF) threshold. At each step, all variants in the current window with VIF exceeding the threshold are removed.

Output 3 channels

#1 prunein tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.prune.in` file	File with IDs of pruned subset of markers that are in approximate linkage equilibrium with each other `*.{prune.in}`

#2 pruneout tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.prune.out` file	File with IDs of excluded variants `*.{prune.out}`

#3 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 19:04:17 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fplink%2Findep/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/plink/indep/blobs/sha256:f21453d256e4641ecb0779371bec8bc26a4d5dcd25e8238f7b23efa81c2bcf81
Size	2.9 KB
Checksum	sha256:f21453d256e4641ecb0779371bec8bc26a4d5dcd25e8238f7b23efa81c2bcf81
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:04:17 (UTC)		1	2.9 KB	-