genepi/nf-gwas
README
nf-gwas is a Nextflow pipeline to run biobank-scale genome-wide association studies (GWAS) analysis. The pipeline automatically performs numerous pre- and post-processing steps, integrates regression modeling from the REGENIE package and currently supports single-variant, gene-based and interaction testing. All modules are structured in sub-workflows which allows to extend the pipeline to other methods and tools in future. nf-gwas includes an extensive reporting functionality that allows to inspect thousands of phenotypes and navigate interactive Manhattan plots directly in the web browser.
The pipeline is tested using the unit-style testing framework nf-test and includes a schema definition to run with Nextflow Tower.
Documentation
Documentation can be found here.
Citation
Please cite our paper if you use nf-gwas:
Schönherr S*, Schachtl-Riess JF*, Di Maio S*, Filosi M, Mark M, Lamina C, Fuchsberger C, Kronenberg F, Forer L. Performing highly parallelized and reproducible GWAS analysis on biobank-scale data. NAR Genom Bioinform. 2024 Feb 7;6(1):lqae015. doi: 10.1093/nargab/lqae015. PMID: 38327871; PMCID: PMC10849172.
Quick Start
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Install Nextflow (>=22.10.4)
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Run the pipeline on a test dataset
nextflow run genepi/nf-gwas -r v1.0.9 -profile test,<docker,singularity,slurm,slurm_with_scratch>
- Run the pipeline on your data
nextflow run genepi/nf-gwas -c <nextflow.config> -r v1.0.9 -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 and was developed at the Institute of Genetic Epidemiology, Medical University of Innsbruck, Austria.
Contact
nf-gwas pipeline parameters
A Nextflow GWAS pipeline.
Total Parameters: 74
Input/output options
1 parameters
All Tests
8 parameters
Single-variant tests only
1 parameters
Gene-based tests only
4 parameters
Interaction tests
3 parameters
Conditional analyses
1 parameters
General options
12 parameters
Pruning step
5 parameters
Quality control of predictions
5 parameters
VCF to PLINK conversion
1 parameters
Prediction step (Regenie Step 1)
4 parameters
Single-variant and gene-based tests (Regenie Step 2)
3 parameters
Single-variant tests only
4 parameters
Gene-based tests only
7 parameters
Interaction tests only
3 parameters
R report
5 parameters
Other options
7 parameters
Launch Pipeline
Run this pipeline using Seqera on top of your own compute.