Oxford Nanopore Output Specifications

This project is intended to contain parsable definitions of Oxford Nanopore software (specifically MinKNOW, Dorado, and EPI2ME) interchange formats.

Currently, this project primarily contains MinKNOW outputs. Further specifications, including additional outputs from EPI2ME and standalone Dorado, are planned for a future release. Until then, details of these projects can be found in the EPI2ME Docs and Dorado Docs.

Public docs

The rendered documentation is available here.

Deploying new docs

Use Mike to deploy a new branch.

First ensure you are on the right branch (for example named release/25.03) and the docs are correct.

Then build and deploy the docs to the gh-pages branch:

> mike deploy [version]

You can also update the latest alias if the branch you are deploying is the latest release:

> mike deploy [version] latest --update-aliases

These commands commit to the gh-pages on your local git repository. You can then push the gh-pages branch to the appropriate remote.

Development

You can set up a local developer build of the documentation by first preparing a python local environment:

pip install -r ./requirements.txt

Then start the documentation in dev mode:

PYTHONPATH=./docs/mkdocs_extensions/ mkdocs serve