nf4ls-materials

A GitHub template repository for delivering the Nextflow for the Life Sciences workshop. When you create a new repository from this template, a GitHub Actions workflow automatically populates it with the full workshop content, with instructor notes removed and your organisation's details substituted in.

Using this template

1. Click Use this template on the GitHub repository and create a new repository under your org/username
2. The template.yml workflow fires automatically on the first push, running cookiecutter to:
   • Populate the repo with the workshop materials from this template
   • Replace repo name, site name, and GitHub username throughout
   • Strip instructor-only notes
   • Set up the MkDocs deploy workflow
3. After a few seconds, your repo will contain the full workshop site, ready to deploy to GitHub Pages.

What the generated repo contains

• Full workshop content (Part 1 and Part 2) from the 2025 Nextflow for the Life Sciences workshop
• MkDocs site with Material theme, auto-deployed to GitHub Pages on push to main
• Setup scripts and sample data for the training environment

Enabling GitHub Pages in the generated repo

1. Go to Settings → Pages in your new repo.
2. Set Source to Deploy from a branch, branch gh-pages, folder / (root).
3. Go to Actions and enable workflows if prompted.

Your site will be published at https://<github_account>.github.io/<repo_name>/.

Acknowledgements

Materials developed by the Sydney Informatics Hub, enabled by Australian BioCommons' BioCLI Platforms Project.

These materials have been developed by:

• Georgie Samaha, Sydney Informatics Hub, University of Sydney
• Fred Jaya, Sydney Informatics Hub, University of Sydney
• Michael Geaghan, Sydney Informatics Hub, University of Sydney
• Giorgia Mori, Australian BioCommons