GWAS SumStats Tools

A toolkit for processing, validating, and formatting GWAS (Genome-Wide Association Studies) summary statistics files for submission to the GWAS Catalog.

It ships as:

gwas-ssf CLI — full-featured command-line tool (Python package on PyPI)
SSF-morph — browser-based UI for formatting and validating single files (no install required)

Repository Layout

gwas-sumstats-tools/
├── src/
│   └── gwas_sumstats_tools/    # Python package (the core library and CLI)
├── apps/
│   └── ssf-morph/              # Browser web app (Pyodide-based)
├── docs/
│   ├── gwas-sumstats-tools-doc/  # Docsify documentation site
│   └── decisions/              # Architecture decision records
├── tests/                      # Pytest test suite
├── deployment/                 # Kubernetes Helm chart
├── dist/                       # Built Python wheel and sdist archives
├── Dockerfile                  # Docker image for the CLI
├── Dockerfile.docs             # Docker image: nginx serving ssf-morph + docs
├── nginx.conf                  # nginx routing config for the Docker image
├── DEPLOYMENT.md               # End-to-end deployment guide
├── pyproject.toml              # uv/PEP 621 project configuration
└── .github/                    # CI/CD pipelines

Folder Descriptions

`src/gwas_sumstats_tools/`

The installable Python package. Exposes a gwas-ssf CLI entry-point and a public Python API.

File / Folder	Purpose
`cli.py`	Typer-based CLI — `read`, `format`, `validate`, `gen-meta` commands
`read.py`	Preview a summary statistics file, extract headers or metadata
`format.py`	Convert tabular files to gwas-ssf standard format
`validate.py`	Validate a file against the gwas-ssf schema
`gen_meta.py`	Auto-generate metadata from a submission form or the GWAS Catalog API
`config.py`	Load and parse the JSON configuration file used by `format`
`constants.py`	Shared constants (field names, defaults)
`utils.py`	Internal helper functions
`interfaces/`	Data-layer abstractions: `data_table.py` (tabular data), `metadata.py` (YAML metadata)
`schema/`	Pydantic/Pandera schemas for data validation and config structure

`apps/ssf-morph/`

A browser-only web app that runs the same Python formatting and validation logic in-browser via Pyodide (Python compiled to WebAssembly). No server or installation needed.

File / Folder	Purpose
`index.html`	Main UI — two-mode wizard (Format / Validate)
`consumer.js`	Event handlers, config form builders, async orchestration
`py-worker.js`	Async wrapper that forwards tasks to the Web Worker
`webworker.js`	Web Worker: initialises Pyodide, mounts the local filesystem, runs Python scripts
`python_bin/`	Python scripts executed inside the browser (read, format, validate)
`wheels/`	Pre-built Python wheels loaded at startup by Pyodide
`Icons/`	UI icon assets

Requires a Chromium-based browser (Chrome, Edge). Single file, max 2 GB.

`docs/gwas-sumstats-tools-doc/`

A Docsify documentation site — plain Markdown files rendered client-side. Covers installation, CLI usage, the web UI guide, a tutorial, and the configuration format.

File / Folder	Purpose
`index.html`	Docsify entry point
`README.md`	Homepage / overview
`install.md`	Installation instructions
`tutorial.md`	Step-by-step tutorial
`CLI_read.md`	CLI: read command reference
`CLI_format.md`	CLI: format command reference
`CLI_validate.md`	CLI: validate command reference
`CLI_gen_meta.md`	CLI: gen-meta command reference
`UI_format.md`	SSF-morph web UI guide
`edit_config.md`	How to write/edit the format config file
`img/`	Images and GIFs used in the docs
`test_data/`	Example input files referenced in the tutorial

`tests/`

Pytest test suite covering CLI, formatting, reading, validation, and utilities.

File	Purpose
`test_cli.py`	End-to-end CLI command tests
`test_format.py`	Unit tests for the format module
`test_read.py`	Unit tests for the read module
`test_validate.py`	Unit tests for the validate module
`test_utils.py`	Unit tests for helper utilities
`prep_tests.py`	Test fixtures and shared setup
`interfaces/`	Tests for the data-layer interfaces

`deployment/`

Kubernetes deployment configuration using Helm.

File	Purpose
`helm/Chart.yaml`	Helm chart metadata
`helm/values.yaml`	Default values (image tag, namespace, resources)
`helm/templates/deployment.yaml`	K8S Deployment resource
`helm/templates/service.yaml`	K8S Service resource
`helm/templates/ingress.yaml`	K8S Ingress resource

`docs/decisions/`

Architecture Decision Records (ADRs) — lightweight design documents explaining why key technical choices were made.

File	Purpose
`0001-validator.md`	Decision record for the validation approach
`0002-deployment.md`	Decision record for the deployment architecture
`0003-uv-package-manager.md`	Migration from Poetry to uv; Python 3.13 and dependency upgrades

`dist/`

Pre-built Python distribution archives (wheels and source tarballs) produced by uv build. The latest wheel is also copied into apps/ssf-morph/wheels/ for use by the browser app.

Quick Start

CLI (pip)

pip install gwas-sumstats-tools      # requires Python 3.13+
gwas-ssf --help

Web UI

Open SSF-morph in Chrome or Edge — no installation required.

Local development

# Install dependencies
uv sync

# Run tests
uv run pytest

# Preview the docs locally
cd docs/gwas-sumstats-tools-doc
python3 -m http.server 3000
# then open http://localhost:3000

Deployment

Two independent release flows:

Flow	Trigger	Produces
PyPI	GitHub Release	Python package on PyPI + updated wheel in apps/ssf-morph
Docs/App	Push to `dev` or git tag via GitLab CI	Docker image → Kubernetes (EBI)

See DEPLOYMENT.md for full details.

Citation:

If you use the NHGRI-EBI GWAS Catalog tool in your research, please refer to the "How to Cite the NHGRI-EBI GWAS Catalog, Data, or Diagrams" section on our website for proper citation guidelines.

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