Nextflow Registry | nf-core/plink/ld@0.0.0-6c4ed3a

nf-core/plink/ld @ 0.0.0-6c4ed3a

LD analysis in PLINK examines genetic variant associations within populations

genetics associations variants

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

Source: nf-core/modules

Authors: @davidebag

Maintainers: @davidebag

LD analysis in PLINK examines genetic variant associations within populations

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

include { PLINK_LD } from 'nf-core/plink/ld'

MIT License

Process

`Name`	`PLINK_LD`

Input 4 channels

#1 tuple

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

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] meta2 is associated to VCF files input
`vcf` file	VCF format input file `.{vcf} \| {vcf.gz}`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] meta is associated to BCF files input
`bcf` file	BCF format input file `*.{bcf}`

#4 tuple

`meta4` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] meta is associated to randomly selected snp files input
`snpfile` file	randomly selected snp identifiers, used to calculate linkage disequilibrium `*.{txt}`

Output 4 channels

#1 ld tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.ld` file	The output of a linkage disequilibrium analysis in PLINK typically includes a table showing variant pairs and their associated LD values, often expressed as R².

#2 log tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.log` file	Log file of the ld process

#3 nosex tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.nosex` file	Ambiguous sex ID file

#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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:37:51 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fplink%2Fld/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/plink/ld/blobs/sha256:65254058f3308fbace5345fc46329a62d24951707fd0900ddbb386f9242de6aa
Size	3.1 KB
Checksum	sha256:65254058f3308fbace5345fc46329a62d24951707fd0900ddbb386f9242de6aa