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

Epistasis in PLINK, analyzing how the effects of one gene depend on the presence of others.

interactions variants regression
Latest version: 0.0.0-6c4ed3a
Total downloads: 11
Source: nf-core/modules
Authors: @davidebag
Maintainers: @davidebag

Summary

Epistasis in PLINK, analyzing how the effects of one gene depend on the presence of others.

Get started

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

include { PLINK_EPISTASIS } from 'nf-core/plink/epistasis'

License

MIT License

Process
Name PLINK_EPISTASIS
Input 4 channels
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ] meta is associated to the PLINK native file 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 file input
vcf file

Variant calling file (vcf)

 *.{vcf}
#3 tuple
meta3 map

Groovy Map containing sample information, e.g. [ id:'test', single_end:false ] meta3 is associated to BCF file input
bcf file

PLINK variant information + sample ID + genotype call binary file

 *.{bcf}
#4 tuple
meta4 map

Groovy Map containing sample information, e.g. [ id:'test', single_end:false ] meta4 is associated to phenotype file input
phe file

PLINK file containing phenotype information. This phenotype information can be read from the third column with the --pheno option or from a specific column with the --pheno-name option.

 *.{phe}
Output 5 channels
#1 epi tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
*.epi.cc file

PLINK epistasis file

 *.{epi.cc}
#2 log tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
*.log file

PLINK epistasis log file

 *.{log}
#3 nosex tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
*.nosex file

Ambiguous sex ID file

 *.{nosex}
#4 episummary tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
*.epi.cc.summary file

PLINK epistasis summary file

 *.{epi.cc.summary}
#5 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 15:37:40 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fplink%2Fepistasis/0.0.0-6c4ed3a/download