https://github.com/nanoporetech/ont-output-specifications
Specifications for output files from MinKNOW, dorado and others
https://github.com/nanoporetech/ont-output-specifications
Last synced: 11 months ago
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Specifications for output files from MinKNOW, dorado and others
- Host: GitHub
- URL: https://github.com/nanoporetech/ont-output-specifications
- Owner: nanoporetech
- Created: 2025-02-07T12:06:27.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-06-05T08:44:22.000Z (about 1 year ago)
- Last Synced: 2025-06-05T09:37:38.791Z (about 1 year ago)
- Language: Python
- Size: 1.23 MB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# 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](https://github.com/nanoporetech/dorado), are planned for a future release. Until then, details of these projects can be found in the [EPI2ME Docs](https://epi2me.nanoporetech.com/epi2me-docs/quickstart/) and [Dorado Docs](https://dorado-docs.readthedocs.io/en/latest/).
## Public docs
The rendered documentation is [available here](https://nanoporetech.github.io/ont-output-specifications/latest/).
## Deploying new docs
Use [Mike](https://github.com/jimporter/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:
```bash
pip install -r ./requirements.txt
```
Then start the documentation in dev mode:
```bash
PYTHONPATH=./docs/mkdocs_extensions/ mkdocs serve
```