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Getting Started

  1. Install Nextflow (>=21.04.0).

  2. Install Docker or Singularity.

  3. Run the pipeline on a test dataset using Docker to validate your installation.

     nextflow run genepi/nf-gwas -r v0.3.5 -profile test,<docker,singularity>
    

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_array               = 'tests/input/example.{bim,bed,fam}'
         genotypes_imputed             = 'tests/input/example.bgen'
         genotypes_build               = 'hg19'
         genotypes_imputed_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 with your configuration file

     nextflow run genepi/nf-gwas -c project.config -r v0.3.5 -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.