Getting Started
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Install Nextflow (>=21.04.0).
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Install Docker or Singularity.
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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
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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 }
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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.