Getting Started

1. Install Nextflow (>=22.10.4)

2. Install Docker or Singularity.

Note for Windows users: This step-by-step tutorial helps you to set up Nextflow on your local machine.

1. Run the pipeline on a test dataset to validate your installation.

    nextflow run genepi/nf-gwas -r <latest-tag> -profile test,docker
   

   Note: Click here to replace the <latest-tag> with the actual version you want to run (e.g. -r v1.0.0).

Run the pipeline on your data

1. Create a Nextflow configuration file (e.g. project.config) and set the required parameters and paths. A complete list of parameters can be found here.

    params {
        project                       = 'test-gwas'
        genotypes_prediction          = 'tests/input/example.{bim,bed,fam}'
        genotypes_association         = 'tests/input/example.bgen'
        genotypes_build               = 'hg19'
        genotypes_association_format  = 'bgen'
        phenotypes_filename           = 'tests/input/phenotype.txt'
        phenotypes_columns            = 'Y1,Y2'
        phenotypes_binary_trait       = false
        regenie_test                  = 'additive'
        annotation_min_log10p         = 2
    }
   

2. Run the pipeline on your data with your configuration file

    nextflow run genepi/nf-gwas -c project.config -r v<[latest tag](https://github.com/genepi/nf-gwas/tags)> -profile <docker,singularity>
   

Note: The slurm profiles require that (a) singularity is installed on all nodes and (b) a shared file system path as a working directory.