nf-core/plink2/indeppairwise @ 0.0.0-6c4ed3a
Summary
Produce pruned set of variants in approximatelinkage equilibrium
Get started
Add the following snippet to your workflow script to include this module.
include { PLINK2_INDEPPAIRWISE } from 'nf-core/plink2/indeppairwise'
License
MIT License
Name
|
PLINK2_INDEPPAIRWISE |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
plink_genotype_file
file
|
PLINK binary genotype table file or PLINK 2 binary genotype table file *.{bed,pgen}
|
plink_variant_file
file
|
PLINK extended MAP file or PLINK 2 variant information file *.{bim,pvar}
|
plink_sample_file
file
|
PLINK sample information file or PLINK 2 sample information file *.{fam,psam}
|
win
integer
|
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. *.{}
|
|---|
step
integer
|
Variant count to shift the window at the end of each step. *.{}
|
|---|
r2
float
|
R squared threshold *.{}
|
|---|
prune_in
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.prune.in
file
|
Variants in linkage equilibrium *.prune.in
|
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
prune_out
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.prune.out
file
|
Excluded variants *.prune.out
|
| Tool | Description | Homepage |
|---|---|---|
| plink2 | Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner | http://www.cog-genomics.org/plink/2.0/ |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:37:58 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fplink2%2Findeppairwise/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/plink2/indeppairwise/blobs/sha256:514bddcf798d7f39e8042483ce136aa877833b6095e56f094a152408046b33f3 |
| Size | 2.9 KB |
| Checksum | sha256:514bddcf798d7f39e8042483ce136aa877833b6095e56f094a152408046b33f3 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:37:58 (UTC) | 3 | 2.9 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:27:06 (UTC) | 3 | 3.0 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:27:44 (UTC) | 3 | 2.9 KB |