Nextflow Registry | nf-core/regenie/step1@0.0.0-bf60969

nf-core/regenie/step1 @ 0.0.0-bf60969

Run REGENIE step 1 to fit whole-genome regression models and emit LOCO predictions

regenie gwas association burden test genomics

Latest version: 0.0.0-bf60969

Total downloads: 0

Source: nf-core/modules

Authors: @lyh970817

Maintainers: @lyh970817

Run REGENIE step 1 to fit whole-genome regression models and emit LOCO predictions

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

include { REGENIE_STEP1 } from 'nf-core/regenie/step1'

MIT License

Process

`Name`	`REGENIE_STEP1`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing genotype information Keep only the genotype analysis identifier in this map REGENIE consumes the staged basename of `plink_genotype_file` as the `--bed` or `--pgen` prefix, so the `.bed/.bim/.fam` or `.pgen/.pvar/.psam` files must share one basename e.g. `[ id:'cohort' ]`
`plink_genotype_file` file	PLINK primary genotype file in BED or PGEN format `*.{bed,pgen}`
`plink_variant_file` file	PLINK variant metadata file in BIM or PVAR format `*.{bim,pvar,zst}`
`plink_sample_file` file	PLINK sample metadata file in FAM or PSAM format `*.{fam,psam}`

#2 tuple

`meta2` map	Groovy Map containing genotype/sample information associated with the phenotype file input Keep only the shared genotype/sample identifier in this map e.g. `[ id:'plink_simulated' ]`
`pheno` file	Phenotype file passed to `--phenoFile` `*.{phe,pheno,txt,tsv}`

#3 tuple

`meta3` map	Groovy Map containing genotype/sample information associated with the covariate input e.g. `[ id:'plink_simulated' ]`
`covar` file	Optional covariate file passed to `--covarFile`; provide `[]` when absent `*.{covar,cov,txt,tsv}`

`bsize` integer	Optional block size passed to `--bsize`; pass `[]` to use the module default of `1000`

Output 4 channels

#1 log tuple

`meta` map	Groovy Map containing genotype information e.g. `[ id:'plink_simulated' ]`
`*.log` file	REGENIE step 1 log file `*.log`

#2 loco tuple

`meta` map	Groovy Map containing genotype/sample information e.g. `[ id:'plink_simulated' ]`
`*.loco.gz` file	REGENIE LOCO prediction files `*.loco.gz`

#3 predictions tuple

`meta` map	Groovy Map containing genotype/sample information e.g. `[ id:'plink_simulated' ]`
`*_pred.list` file	REGENIE prediction list file `*_pred.list`

#4 versions_regenie tuple

`${task.process}` string	The process the versions were collected from
`regenie` string	The tool name
`regenie --version 2>&1 \| sed -n "1{s/^v//;s/\.gz$//;p}"` eval	The command used to generate the version of the tool

Tool	Description	Homepage
regenie	Regenie is a C++ program for whole genome regression modelling of large genome-wide association studies (GWAS).	https://rgcgithub.github.io/regenie/

Version	0.0.0-bf60969
Commit ID	bf60969a3abb40d294cffd5105f574637bfa6260
Release Date	21 May 2026 15:00:58 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fregenie%2Fstep1/0.0.0-bf60969/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/regenie/step1/blobs/sha256:e4b964ffc66570b7bc153278c9f2b91059f6d56372679000a2cdd14066505f5b
Size	4.0 KB
Checksum	sha256:e4b964ffc66570b7bc153278c9f2b91059f6d56372679000a2cdd14066505f5b