abought/nf-executor

nf-executor

A command and control node for a microservice that runs multiple nextflow workflows.

This does not interact with users and should not be exposed to the public internet. It handles LAUNCHING and MONITORING of (many) separate workflow processes. It is the job of the web application to translate user inputs into the options expected by nextflow.

Setup (for local development)

Initial installation

python3 -mvenv .venv
pip3 install -r requirements/local.txt 

Then run the database migrations to create the DB and schema:

python manage.py migrate --settings=config.settings.local

For local development, you will need Nextflow installed. This demo was written using Nextflow version > 23.04.2 and Python 3.11.

In the initial prototype, you may need to explicitly edit some settings in config.settings (local and base). Particularly referencing file locations.

Running

Currently, only a basic development mode is implemented (for prototyping purposes). In the future, local and production containers will be provided.

python manage.py runserver --settings=config.settings.local

Run unit tests

python manage.py test --settings=config.settings.local

Management commands

Database migrations:

python manage.py makemigrations --settings=config.settings.local
python manage.py migrate --settings=config.settings.local

Interactive debugging shell:

python manage.py shell --settings=config.settings.local