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The docs/ folder has the MarkDown content that is rendered to https://bioexcel.github.io/cwl-best-practice-guide/ by GitHub pages.

A file like intro.md appears rendered as https://bioexcel.github.io/cwl-best-practice-guide/intro You may crosslink pages using relative links like [background](background.md) - the extension .md is replaced with .html in rendering.

Note that files outside docs are not accessible within github.io and must be linked to by absolute URLs, e.g. https://github.com/bioexcel/cwl-best-practice-guide/blob/master/example/

It is more important that pages render well at https://bioexcel.github.io/cwl-best-practice-guides/ 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 (README.md) 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 README.md (alternatively index.md) - 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.

References

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

{% include list.liquid all=true %}

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BioExcel Best Practice Guide: Creating workflows with Common Workflow Language

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