New updated List of User Guide Issues

Making a list of existing user guides issues to help with the upcoming Outreachy project and well as help sort out what is left after @kinow recent update work. The new structure ticket maybe have information about where some of these additions will go - can check that here-https://github.com/common-workflow-language/user_guide/pull/226 Also, "nubs" and "To Dos" have been placed as comments in the User Guide itself to let you know where things might be added.

**v1.1, v1.2 Features**

- [ ] Mention version mixing; and explain when and how to use cwl-upgrader, https://github.com/common-workflow-language/user_guide/issues/188
- [ ] NetworkAccess: Need example to show how to Indicate whether a process requires outgoing IPv4/IPv6 network access and what happens if not indicated and ]network access is need but isn't available, https://github.com/common-workflow-language/user_guide/issues/249

**Expanding/Revising Existing Content**

***In Introduction/Prerequisite***
- [ ] Include where the cwl-runner source is? Note from Bruno when writing this section - "I couldn't find in PYPI ait points to the CWL project: https://github.com/common-workflow-language/cwltool/tree/main/cwlref-runner", NO CURRENT TICKET FOR THIS , but has a note in the markdown as a TODO

***In Introduction/Basic Concepts***
- [ ] Add a link to the Core Concepts -> Requirements section, NO CURRENT TICKET - but has a note in the markdown as a TODO

***In Topics/CommandLineTool***
- [ ] 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), No existing ticket just a common bottom of the markdown

***In Topics/ExpressionTool***

- [ ] Explain better with more examples (need to get more information for this)

***In Topics/Inputs***

- [ ] Explain its fields, such as default, valueFrom, etc., https://github.com/common-workflow-language/common-workflow-language/issues/359
- [ ] Exclusive parameters, https://github.com/common-workflow-language/user_guide/issues/162 _Maybe fixed by waiting pull request_
- [ ] 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-languag/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

***Location-TBD***

- [ ] Improve Scatter documentation, https://github.com/common-workflow-language/user_guide/issues/232.
- [ ] Expand Section on Containers to include Singularity, https://github.com/common-workflow-language/user_guide/issues/231
- [ ] Running cwltool in a container, https://github.com/common-workflow-language/user_guide/issues/231
- [ ] Update and clarify existing docker example, https://github.com/common-workflow-language/user_guide/issues/231 and https://github.com/common-workflow-language/user_guide/issues/119 , https://github.com/common-workflow-language/user_guide/issues/190
- [ ] Explain about running cwltool inside docker containers, https://github.com/common-workflow-language/user_guide/issues/231
- [ ] Make a better example for showing metadata instead of running wordcount on a bam file, https://github.com/common-workflow-language/user_guide/issues/190
- [ ] Add content for mutually exclusive inputs, https://github.com/common-workflow-language/user_guide/issues/229
- [ ] Show how to extract a specific element from an array, https://github.com/common-workflow-language/user_guide/issues/184
- [ ] Explain multi-dimensional scattering and give an example, https://github.com/common-workflow-language/user_guide/issues/181
- [ ] Highlight the major features of cwltool (e.g. --validate, --parallel ), Note: Some of this has been done but some left to do. , https://github.com/common-workflow-language/user_guide/issues/166
- [ ] Explain Shell Command - https://github.com/common-workflow-language/user_guide/issues/159 Looks like it should so in the nub of the "4.12. Requirements and Hints"
- [ ] Explain how to reference a local script, https://github.com/common-workflow-language/user_guide/issues/158 Note: this doesn't have placement in the new structure - so maybe FAQs?

**Formatting Issues**

- [ ] Table of Contents doesn't show important workflow subsections, https://github.com/common-workflow-language/user_guide/issues/252
- [ ] Extra box on left-hand-side table of contents, https://github.com/common-workflow-language/user_guide/issues/244
- [ ] Adjust wording to use Topics instead of Core Concepts in Intro - https://github.com/common-workflow-language/user_guide/issues/255

**Needs Clarification or More Information**

- [ ] Explain drawback with docker, https://github.com/common-workflow-language/user_guide/issues/239 - Some of this is already explained. in User Guide but not the singularity/docker interaction.
- [ ] Guidelines or Best Practices for the scope of command line tools. , https://github.com/common-workflow-language/user_guide/issues
- [ ] Example for using expressions with exclusive parameter (an example has to be made for this issue), https://github.com/common-workflow-language/user_guide/issues
- [ ] Need to explain how to add conformance tests and/or add them for new example, https://github.com/common-workflow-language/user_guide/issues/254
- [ ] - [ ] Fix the missing link the graph below (CWL command-line tool.) 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, NO CURRENT TICKET FOR THIS, but it has a note in the markdown as a TODO
- [ ] 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, No current ticket for this, but it has a note in the markdown as a TODO
- [ ] 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, NO CURRENT TICKET, but it has note in the markdown as a TODO
- [ ] 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

**May Be Fixed by Outstanding Pull Requests**
- [ ] Show how to transpile newer Javascript code for ECMAScript 5.1, https://github.com/common-workflow-language/user_guide/issues/245

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