dear-ore / commonworkflowlanguage-user_guide Goto Github PK

User guide for CWL v1.2.0

Original source: https://github.com/common-workflow-language/common-workflow-language/blob/a2a8a08b8c8d56f8f2ca6284ca4e9cbf23d19346/v1.0/UserGuide.yml

We welcome all contributions to improve the materials! Maintainers will do their best to help you if you have any questions, concerns, or experience any difficulties along the way. To edit the user guide:

We'd like to ask you to familiarize yourself with our Contribution Guide.

We must use CWL standards or CWL open standards when talking about CWL. We must use specification only when talking specifically about the CWL specification document.

Whenever a page is updated we must verify that it does not break existing links. The make html command will fail if Sphinx detects broken links. It only works for links managed by Sphinx (i.e. table of contents links, or links to Markdown pages). For simple HTML links (e.g. < href=> or markdown external links) pull request reviewers must verify that links are still working after the change.

Use “tool description” not “tool wrapper” for describing the first argument given to the cwl-runner or cwltool commands.

To include code into a Markdown file you have two options. For external files use the following command:

```{literalinclude} /_includes/cwl/hello_world.cwl
:language: cwl
```

For code examples in the same page, you can use fence blocks.

```bash
echo "Hello world"
```

If you would like to customize the syntax highlighting styles you will have to customize the Sphinx and Pygments settings. To preview Pygments output with different styles, use their Pygments demo tool.

Sphinx and the theme are configured to auto-generate anchor slug links for sections. So sections like ## cwl standard are translated into an anchor link #cwl-standard.

If you are having trouble with links to sections or code blocks, it might be due to duplicated sections, or to spaces or other characters. To preview the generated links, use the myst-anchors tool.

$ (venv) myst-anchors basic-concepts.md
<h1 id="basic-concepts"></h1>
<h2 id="the-cwl-standard"></h2>
<h2 id="implementations"></h2>
<h2 id="cwl-objects-model"></h2>

You can also create reference anchor links anywhere on the page with (test)=, which can be used in the page as #test (these do not appear in the myst-anchor output).

Links to anchors in pages work only for Sphinx's autogenerated anchor links. If you have an anchor for, for example, a code-block, that might cause the build to fail: executablebooks/MyST-Parser#564

We use MyST Parser with Sphinx. This gives us the best of both Sphinx and Markdown, while also supporting reStructuredText, Sphinx, and MyST extensions.

For convenience, we have the currently supported version of the specification as a constant in conf.py. We have it in two forms:

• Markdown preformatted, i.e. `v0.0` which is formatted as v0.0
• Plain text, i.e. v0.0

Note that String Substitutions do not work with links. As workaround, you can use string formatting or replacements.

The CWL {{ cwl_version  }} Specification: {{ '<https://www.commonwl.org/{}/>'.format(cwl_version_text) }}

For more:

• https://myst-parser.readthedocs.io/en/latest/syntax/optional.html#substitutions-with-jinja2
• https://myst-parser.readthedocs.io/en/latest/syntax/optional.html#substitutions-and-urls
• executablebooks/MyST-Parser#279

A list of contributors to these materials can be found in AUTHORS

To cite these materials, please consult with CITATION