nf-core pipeline · gwas
nf-core/gwas
A Nextflow pipeline under development for conducting genome-wide association studies.
What nf-core/gwas is
nf-core/gwas is a bioinformatics pipeline designed to perform genome-wide association studies (GWAS). It was originally written by Chris Wyatt, Fernando Duarte, and Maxime Laurent within the nf-core community framework.
The pipeline is currently under construction. In its documented development state, it is structured to take a sample sheet as input and process raw sequencing data through quality control stages.
What the pipeline does
The pipeline is executed using Nextflow, accepting a comma-separated values (CSV) sample sheet via the input parameter and writing results to a designated output directory. One of the default steps in the workflow is presenting quality control reports for raw reads using MultiQC.
Key facts
- Pipeline status
- Under construction
- Original authors
- Chris Wyatt, Fernando Duarte, Maxime Laurent
- Workflow manager
- Nextflow
- Input format
- Sample sheet (CSV)
- Quality control tool
- MultiQC
Run it here
The research agent runs nf-core/gwas with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
Strengths and limits
Good at
- Integrates MultiQC to report quality control metrics for raw sequencing reads.
- Standardised within the nf-core Nextflow ecosystem.
Watch out for
- The workflow is explicitly under construction and incomplete.
- Pipeline steps, inputs, and association testing tools are not yet fully specified in the documentation.
Questions
Can I run nf-core/gwas without my own cluster?
The research agent runs nf-core/gwas with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
What licence is nf-core/gwas under?
MIT, like every nf-core pipeline.
What is the current status of nf-core/gwas?
The pipeline is currently under construction and in active development.
Who are the original authors of nf-core/gwas?
It was originally written by Chris Wyatt, Fernando Duarte, and Maxime Laurent.
What quality control tools are included in the workflow?
The pipeline uses MultiQC to present quality control results for raw sequencing reads.
How to cite it
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
Written from nf-core/gwas's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.