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This is the Github repository holding the raw markdown for the BioExcel CWL engines guide which is rendered here:

The docs/ folder has the MarkDown content that is rendered to by GitHub pages.

Note that files outside docs are not accessible within and must be linked to by absolute URLs, e.g.

It is more important that pages render well at than in this preview within the GitHub repository, as some MarkDown features only apply to the GitHub Pages (e.g. the {:toc} macro and).

Using the jekyll-rtd-theme

Note that the specification 1.1 onwards uses split files for different sections, these are indexed by the RunDocs theme aka rundocs/jekyll-rtd-theme. The --- preamble is required on all *.md files to help the theme, e.g.:

layout: default
title: Introduction
excerpt: |
  This is the introduction.
sort: 5

Tip: Only add sort for numbered sections. Unfortunately the number is shown as-is (no GOTO 20 tricks), leading to frequent renumbering.

Hiding a section

To hide a section ( or other file from the main table of content, e.g. a draft, add exclude: true to its preamble:

layout: default
exclude: true
title: Draft section

This is checked by a crude filter in the overriding _includes/reset/site_pages.liquid. This file might need to be moved/updated when upgrading the theme.

Sections and child pages

Note that although section folders have a (alternatively - it is not generally shown in the left-hand menu, only in the breadcrumb. It is therefore recommended to make these index page minimal and only include a list of subpages of that section, using this Liquid include:

{% include list.liquid all=true %}

This is also helpful for navigating drafts as exclude: true does not show their sections in the left-hand menu.

Theme config

The theme is locked to a fixed version in _config.yml to avoid unexpected upgrade surprises. This file also specifies some site-wide properties like copyright.


The _includes/references.liquid file includes Markdown hyperlink references that can be used on shortform, e.g. [CreativeWork] gets expanded to [CreativeWork]( or [creative work][CreativeWork] becomes [creative work]( This only works on *.md pages that have the {% include references.liquid %} footer.

{% include list.liquid all=true %}


BioExcel Best Practice Guide: Workflow Engines for Common Workflow Language







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