depmap-omics-wgs

This repository contains WDL workflows and a Python module to continuously run workflows on new WGS samples.

Installation

1. Install the required system dependencies:

   • pyenv
   • Poetry
   • pre-commit

2. Install the required Python version (3.12.1):

   pyenv install "$(cat .python-version)"

3. Confirm that python maps to the correct version:

   python --version
   

4. Set the Poetry interpreter and install the Python dependencies:

   poetry env use "$(pyenv which python)"
   poetry install

5. Copy env.dist into a new file .env and fill it out:

   • HASURA_URL can be copied from ariadne-prod.yml
   • HASURA_ADMIN_SECRET can be copied from the hasura-admin-secret-prod secret

Credentials

Download a service account key for omics-pipeline-runner and set the GOOGLE_APPLICATION_CREDENTIALS environment variable to its location on your filesystem. This will simulate the permissions available inside the remote execution context.

Execution

TODO

Development

Run pre-commit run --all-files to automatically format your code with Ruff and check static types with Pyright.

Whenever possible, function/method arguments and return values should be validated with Pydantic or Pandera (if a data frame).

GraphQL code generation

This repo uses ariadne-codegen to generate the gumbo_gql_client module. It uses the folder of GraphQL queries (./gql) and the current GraphQL schema for a particular Gumbo environment to generate all of the Python classes, Pydantic models, and query/mutation methods for interacting with the Gumbo GraphQL Service. To regenerate the module using the current production schema:

HASURA_ADMIN_SECRET=... poetry run ariadne-codegen --config ariadne-prod.toml

Scratch files

Some Python files in ./scratch are available to seed the Gumbo task results table.