joon-klaps / website-nf-core

Code and files for the main nf-core website.

nf-co.re

This repository contains code for the nf-core website: http://nf-co.re/

Packages used

Here's how the website is built:

• Language: Javascript
• Frameworks:
  • Astro (static site generator),
  • Svelte (interactive components),
  • Bootstrap 5.3 (CSS framework)
• Tools:
  • npm (package manager)

Development

Getting the code

To make edits to the website, fork the repository to your own user on GitHub and then clone to your local system.

gh repo fork nf-core/website nf-core_website
cd nf-core_website/

Installing dependencies

The website is built using Astro, a static site generator. To install the dependencies, run:

npm install

Running a local server

Ok, you're ready! To run the website locally, just start astro dev mode:

npm run dev

You should then be able to access the website in your browser at http://localhost:4321/.

File structure

We follow Astro's file structure for the website. The main files are:

• src/pages/ - Astro pages
• src/content/ - Astro content collections (markdown files for events, docs)
• src/components/ - Astro/Svelte components
• src/layouts/ - HTML layouts
• src/styles/ - (S)CSS stylesheets
• public/ - Static files (images, json files etc)

Updating the JSON files and cached markdown

Much of the site is powered by the JSON files in /public and the cached markdown files (from the pipeline docs) in /.cache.

They come pre-built with the repository, but if you want to rebuild them then you'll need to run the following commands. Note that you need to add a GITHUB_TOKEN inside a .env file to avoid hitting API limits (too early). See instructions on how to get a GitHub OAuth token (the token only needs the public_repo permission).

npm run build-pipeline-json
npm run build-component-json
npm run build-cache-force

Tools API docs

Tools docs are built using GitHub Actions on the nf-core/tools repo using Sphinx. These actions sync the built HTML files via FTP.

Contribution guidelines

If you are looking forward to contribute to the website or add your institution to the official list of contributors, please have a look at the CONTRIBUTING.md.

Community

If you have any questions or issues please send us a message on Slack.

Credits

Phil Ewels (@ewels) built the initial website, but there have been many contributors to the content and documentation. Matthias Hörtenhuber (@mashehu) worked on the concept and code for the new website rewrite.

See the repo contributors for more details.

Kudos to the excellent npm website, which provided inspiration for the design of the pipeline pages.