/nf-gwas

A nextflow pipeline to perform genome-wide association studies using regenie.

Primary LanguageNextflowMIT LicenseMIT

nf-gwas

nf-gwas

A nextflow pipeline to perform genome-wide association studies (GWAS) using regenie.

Documentation

Documentation can be found here.

Quick Start

  1. Install Nextflow (>=21.04.0)

  2. Run the pipeline on a test dataset

nextflow run genepi/nf-gwas -r v0.3.5 -profile test,<docker,singularity,slurm,slurm_with_scratch>
  1. Run the pipeline on your data
nextflow run genepi/nf-gwas -c <nextflow.config> -r v0.3.5 -profile <docker,singularity,slurm,slurm_with_scratch>

Please click here for available test config files.

Development

git clone https://github.com/genepi/nf-gwas
cd nf-gwas
docker build -t genepi/nf-gwas . # don't ignore the dot
nextflow run main.nf -profile test,development

License

nf-gwas is MIT Licensed.

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