nf-core/plink/gwas @ 0.0.0-6c4ed3a
Summary
Generate GWAS association studies
Get started
Add the following snippet to your workflow script to include this module.
include { PLINK_GWAS } from 'nf-core/plink/gwas'
License
MIT License
Name
|
PLINK_GWAS |
|---|
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}
|
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}
|
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}
|
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}
|
log
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.log
file
|
PLINK GWAS association log file *.{log}
|
assoc
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.assoc
file
|
PLINK GWAS association file *.{assoc}
|
nosex
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.nosex
file
|
PLINK GWAS association file that retains phenotypes for samples with ambiguous sex. Produced with the option --allow-no-sex *.{nosex}
|
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 15:37:46 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fplink%2Fgwas/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/plink/gwas/blobs/sha256:883e1e3d986736c94f8a6d7368ca1e17b908e0be58b2630ed226c39c16f696f5 |
| Size | 3.3 KB |
| Checksum | sha256:883e1e3d986736c94f8a6d7368ca1e17b908e0be58b2630ed226c39c16f696f5 |