gwas-pipeline

gwas-pipeline is an installable Python package that wraps a 9-step GWAS tutorial workflow behind a single CLI.

It keeps the original step-by-step tutorial layout, but also provides a package-first interface:

gwas-pipeline step1 ...
gwas-pipeline step2 ...
...
gwas-pipeline step9 ...

What is included

• packaged implementations for step1 to step9
• thin legacy wrapper scripts in gwas_step*_project/
• server-focused runbooks and command examples
• a doctor command for checking environment dependencies

Install

Install from PyPI:

pip install gwas-pipeline

Install from a local checkout for development:

pip install -e .

Quick Start

gwas-pipeline --help
gwas-pipeline doctor --profile plink_env
gwas-pipeline step1 --help
gwas-pipeline step8 --help
python -m gwas_pipeline step9 --help

CI

GitHub Actions runs a small smoke-test suite on pushes and pull requests to make sure the packaged CLI, step registry, and legacy wrappers still load.

Releases can also be created from tags such as v0.3.1; see RELEASING.md for the minimal release flow.

Repository Layout

• src/gwas_pipeline/ Packaged step implementations and CLI entrypoints.
• gwas_step1_project/ to gwas_step9_project/ Legacy-compatible wrappers and per-step tutorial READMEs.
• PACKAGE_COMMANDS.md Copy-paste command examples for all steps.
• SERVER_GWAS_RUNBOOK.md Short command-first server runbook.
• server_setup.md Conda environment, install, and deployment notes.
• RELEASING.md Minimal tag and GitHub Release process.

Tested Status

The tutorial workflow has been tested step-by-step on server.

• step1 Real public FASTQ subset plus real chr22.fa
• step2 Real chr22-region VCF converted to PLINK
• step3 Real GFF plus synthetic GWAS result for logic validation
• step4 Synthetic GWAS result for plotting validation
• step5 to step8 Real public human chr22 / COMT-region inputs
• step9 Real sample geography tables

Notes

• This repository is intentionally limited to the GWAS tutorial package.
• The separate gwas_postgwas_tools project is not included here.
• gwas-pipeline is the primary CLI; the old step scripts remain for compatibility with the original tutorial structure.