Australian BioCommons: customising nf-core workshop series

Workshop title: introduciton to nf-core and customising it for your research.

How to use

1. Edit index.qmd to change the main landing page. This is basically a markdown file.
2. Edit or create setup.qmd to change the Setup instruction pages. Same - basically a md file.
3. Edit _quarto.yml to change the dropdown menu options.
4. Add additional *.md files to the root dir to have them converted to html files (and add them to _quarto.yml to make them navigable), if you'd like.

If you want to use the command line instead of VSCode/RStudio (as described below), run the below commands (after activating the correct Python environment, if needed)

quarto render
# First time you create the file, add them to be tracked by github, e.g.
git add docs/*
git commit -am "your comments"
git push

You can browse the result locally by exploring the html files created (note: sometimes figures display locally but not on web and the other way around too.)

For main "content" in md/qmd

1. Create files in the notebooks folder (for example notebooks/1_cont.md). Have a look at what the syntax for Challenges, Objectives, Key Points and Questions is supported in 0.0.0_template.md, and use similar syntax across other .md files where needed.
2. Add links to your content to the navigation configuration in _quarto.yml. For example, to link to the rendered page for notebooks/1_cont.md, add a link to notebooks/1_cont.html in _quarto.yml
3. Type quarto render in the terminal - or use VSCode's 'Render Quarto project' command using the command pallette instead.