genepi/nf-gwas — reverse-engineered prompt

Build me a reproducible Nextflow pipeline for large scale genome wide association studies, like something a biobank team could run on real genotype and phenotype data.

I want it to handle the messy setup around GWAS automatically, including input checks, preparation steps, regression modeling with REGENIE, and clean output folders. It should support single variant tests, gene based tests, and interaction testing. Please include a small test profile so I can run it end to end with example data, plus configs for common ways people run this, like Docker, Singularity, and SLURM.

The most important part is that the results are easy to review. Generate a browser based report where I can browse many phenotypes, inspect summary results, and open interactive Manhattan plots. Also include clear documentation, example config files, a citation file, and basic tests so other researchers can trust and extend the pipeline.

Look up current Nextflow and nf test docs online if you need to.