List of To-Dos in the User Guide

**_In conf.py_**
- [ ] maybe write our own lexer to customize tokens, keywords, etc?

**_In cwl_tests.yml_**
- [ ] The old section 23-scatter-workflow had workflows, but no conformance tests?
Maybe add them here, they are now in workflows:
- hello_world.cwl
- hello_world_to_stdout.cwl
- scatter-job.cwl
- scatter-nested-workflow.cwl
- scatter-two-steps.cwl
- scatter-workflow.cwl
- wc-tool.cwl

**_In Introduction/Basic Concepts_**
- [ ] add a link to the Core Concepts -> Requirements section below?

**_In Topics/Best Practices_**
- [ ] Writing CWL workflows (include existing docs from https://github.com/common-workflow-library/cwl-patterns/blob/main/README.md)
- [ ] FAIR best practices with CWL
- [ ] Docker best practices with CWL - https://github.com/common-workflow-language/common-workflow-language/issues/347

**_In Topics/CommandLine Tool_**
- [ ] Fix the missing link the graph below. We cannot have it here as this file is included in two other files. Sphinx prohibits it for the case where this could lead to duplicate anchors in a page (e.g. single-html). :name: command-line-tool-graph
- [ ] Fix the missing link the code below. We cannot have it here as this file is included in two other files. Sphinx prohibits it for the case where this could lead to duplicate anchors in a page (e.g. single-html). :name: echo.cwl
- [ ] Spaces in commands https://github.com/common-workflow-language/user_guide/issues/39
- [ ] Arguments (tell the reader the different use cases for arguments and inputs, tell them there is a section about inputs)

**_In Topics/Custom Types_**
- [ ] https://github.com/common-workflow-language/user_guide/issues/155
- [ ] Maybe show an example with booleans, pros and cons - https://github.com/common-workflow-language/user_guide/issues/89
- [ ] https://github.com/common-workflow-language/user_guide/issues/386
- [ ] Document corner cases & workarounds - https://github.com/common-workflow-language/common-workflow-language/issues/241

**_In Topics/Expression Tool_**
- [ ] Explain better with more examples.
- [ ] Fix the missing link the graph below. We cannot have it here as this file is included in two other files. Sphinx prohibits it for the case where this could lead to duplicate anchors in a page (e.g. single-html). :name: expression-tool-graph
- [ ] Fix the missing link the code below. We cannot have it here as this file is included in two other files. Sphinx prohibits it for the case where this could lead to duplicate anchors in a page (e.g. single-html). :name: uppercase.cwl

**_In Topics/Inputs_**
- [ ] Explain its fields, such as default, valueFrom, etc. - https://github.com/common-workflow-language/common-workflow-language/issues/359
- [ ] Optional Inputs https://github.com/common-workflow-language/user_guide/issues/44
- [ ] Several ways of defining inputs/arguments to tools and workflows - https://github.com/common-workflow-language/user_guide/issues/33
- [ ] Using an input output in another input - https://github.com/common-workflow-language/user_guide/issues/90
- [ ] How to use linkMerge - https://github.com/common-workflow-language/user_guide/issues/117 (or maybe move to Advanced?)
- [ ] Secondary files - https://github.com/common-workflow-language/common-workflow-language/issues/270

**_In Topics/Outputs_**
- [ ] Creating files at runtime - https://github.com/common-workflow-language/user_guide/issues/134

**_In Topics/Requirements and Hints_**
- [ ] InlineJavascriptRequirement
- [ ] Maybe list cases where it is not really necessary? e.g. https://github.com/common-workflow-language/common-workflow-language/issues/389
- [ ] Covered by the **episode 13** of the current User Guide - https://www.commonwl.org/user_guide/13-expressions/index.html
- [ ] InitialWorkDirRequirement
- [ ] Staging Files (a common topic, and appears in questions on discourse/element... maybe it deserves a more prominent location?)
- [ ] Writable inputs - https://github.com/common-workflow-language/user_guide/issues/36
- [ ] Creating files at runtime, from **episode 14** of the current User Guide - https://www.commonwl.org/user_guide/14-runtime/index.html
- [ ] There is a whole **episode 15** in the current User Guide about it - https://www.commonwl.org/user_guide/15-staging/index.html
- [ ] DockerRequirement
- [ ] Covered in the **episode 7** of the current User Guide - https://www.commonwl.org/user_guide/07-containers/index.html
- [ ] SchemaDefRequirement and input schemas
- [ ] The **episode 19** from the current User Guide covers it - https://www.commonwl.org/user_guide/19-custom-types/index.html
- [ ] ShellCommandRequirement - https://github.com/common-workflow-language/user_guide/issues/159
- [ ] SoftwareRequirement - From the **20** from the current User Guide - episode https://www.commonwl.org/user_guide/20-software-requirements/index.html
- [ ] MultipleInputFeatureRequirement
- [ ] Also in **episode 24** of the current User Guide - https://www.commonwl.org/user_guide/24_conditional-workflow/index.html
- [ ] SubworkflowFeatureRequirement
- [ ] Also in **episode 22** of the current User Guide - https://www.commonwl.org/user_guide/22-nested-workflows/index.html
- [ ] ScatterFeatureRequirement
- [ ] Also in **episode 23** of the current User Guide - https://www.commonwl.org/user_guide/23-scatter-workflow/index.html

**_In Topics/Workflows_**
- [ ] Fix the missing link the graph below. We cannot have it here as this file is included in two other files. Sphinx prohibits it for the case where this could lead to duplicate anchors in a page (e.g. single-html). :name: workflow-graph
- [ ] Fix the missing link the code below. We cannot have it here as this file is included in two other files. Sphinx prohibits it for the case where this could lead to duplicate anchors in a page (e.g. single-html). :name: echo-uppercase.cwl
- [ ] Fix the missing link the code below. We cannot have it here as this file is included in two other files. Sphinx prohibits it for the case where this could lead to duplicate anchors in a page (e.g. single-html). :name: echo-uppercase-single-file.cwl
- [ ] add a link to the page about SubworkflowFeatureRequirement
- [ ] The link below is for a previous commit with the workflow above. Ideally, I think we should either use `cwltool`or Python to add the graph here. Or, maybe re-create the graph for the latest main version?
- [ ] Scatter
- [ ] ScatterMethod https://github.com/common-workflow-language/user_guide/issues/29
- [ ] Also in the **episode 23** of the current User Guide - https://www.commonwl.org/user_guide/workflows/index.html
- [ ] Subworkflows/nested workflows
- [ ] Covered in the **episode 22** from the current User Guide - https://www.commonwl.org/user_guide/workflows/index.html
- [ ] Conditionals https://github.com/common-workflow-language/user_guide/issues/191 & https://github.com/common-workflow-language/user_guide/issues/188
- [ ] Also in the **episode 24** of the current User Guide - https://www.commonwl.org/user_guide/24_conditional-workflow/index.html