nf-core/plink/indep @ 0.0.0-6c4ed3a
Summary
Produce a pruned subset of markers that are in approximate linkage equilibrium with each other.
Get started
Add the following snippet to your workflow script to include this module.
include { PLINK_INDEP } from 'nf-core/plink/indep'
License
MIT License
Name
|
PLINK_INDEP |
|---|
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. |
|---|
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}
|
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}
|
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 15:37:48 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fplink%2Findep/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/plink/indep/blobs/sha256:1124c5c1543f2df67c04ddc0495b9c056fbed29fc08e49991241e68d8ab3a751 |
| Size | 2.9 KB |
| Checksum | sha256:1124c5c1543f2df67c04ddc0495b9c056fbed29fc08e49991241e68d8ab3a751 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:37:48 (UTC) | 3 | 2.9 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:26:56 (UTC) | 4 | 2.9 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:27:30 (UTC) | 3 | 2.9 KB |