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nf-gwas

nf-gwas nf-test

This cloud-ready GWAS pipeline allows you to run single variant tests and gene-based tests using regenie in an automated and reproducible way. The pipeline outputs tabixed association results (e.g. for LocusZoom), gene-annotated tophits and an interactive HTML report including numerous statistics and plots (e.g. Manhattan Plat, QQ-Plot by MAF).

Documentation

Documentation can be found here.

Quick Start

  1. Install Nextflow (>=21.04.0)

  2. Run the pipeline on a test dataset

nextflow run genepi/nf-gwas -r v0.5.1 -profile test,<docker,singularity,slurm,slurm_with_scratch>
  1. Run the pipeline on your data
nextflow run genepi/nf-gwas -c <nextflow.config> -r v0.5.1 -profile <docker,singularity,slurm,slurm_with_scratch>

Please click here for available test config files.

Development

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-test

nf-gwas makes use of nf-test, a unit-style test framework for Nextflow.

cd nf-gwas
curl -fsSL https://code.askimed.com/install/nf-test | bash
./nf-test test

License

nf-gwas is MIT Licensed.

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