Getting Started

Install Nextflow (>=21.04.0).
Install Docker or Singularity.
Run the pipeline on a test dataset using Docker to validate your installation.
```
 nextflow run genepi/nf-gwas -r v0.5.2 -profile test,<docker,singularity>
```

Run the pipeline on your data

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
 }

Run the pipeline with your configuration file

 nextflow run genepi/nf-gwas -c project.config -r v0.5.2 -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.