New updated List of… | common-workflow-language/user_guide

Inizia esaminando la checklist di questa issue e la nuova struttura proposta in pull request 226, quindi controlla le issue di User Guide e le note TODO di markdown referenziate. Questa issue sarà completa solo quando il lavoro rimanente sulla guida sarà definito in elementi attuabili e l’elenco rifletterà accuratamente ciò che è ancora necessario.

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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