A nextflow pipeline to perform genome-wide association studies (GWAS) using regenie.
Documentation can be found here.
-
Install Nextflow (>=21.04.0)
-
Run the pipeline on a test dataset
nextflow run genepi/nf-gwas -r v0.3.5 -profile test,<docker,singularity,slurm,slurm_with_scratch>
- 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.
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
nf-gwas is MIT Licensed.