Various fixes, updated debug.md to use new format

[alexiswl]

• Removed WSL2 hints in MacOS and linux setups
• Added cwl files for debug markdown and reference from markdown instead.
• Updated challenges to use headers for challenges, also added 'peppers' to determine how challenging a task is.

[github-actions]

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🤖 This automated message can help you check the rendered files in your submission for clarity. If you have any questions, please feel free to open an issue in {sandpaper}.

If you have files that automatically render output (e.g. R Markdown), then you should check for the following:

• 🎯 correct output
• 🖼️ correct figures
• ❓ new warnings
• ‼️ new errors

Rendered Changes

🔍 Inspect the changes: https://github.com/umccr/cwl-novice-tutorial/compare/md-outputs..md-outputs-PR-1

The following changes were observed in the rendered markdown documents:

 02-shell_to_cwl.md                                 |  17 +-
 03-dependency_graphs.md                            |   7 +-
 04-reusing_tools.md                                |   7 +-
 debug.md => addendum-01-debug.md                   | 276 +++++++++++++--------
 .../rna_seq_workflow_fieldname_fail.cwl (new)      |  41 +++
 files/debug/rna_seq_workflow_type_fail.cwl (new)   |  41 +++
 .../debug/rna_seq_workflow_varname_fail.cwl (new)  |  41 +++
 files/debug/rna_seq_workflow_with_format.cwl (new) |  41 +++
 files/debug/tab-error.cwl (new)                    |  56 +++++
 .../workflow_input_undefined_format.yaml (new)     |   6 +
 files/linux_setup.Rmd                              |   4 -
 files/macos_setup.Rmd                              |   2 -
 files/windows_setup.Rmd                            |   5 +-
 md5sum.txt                                         |  39 +--
 more_info.md                                       |   5 +-
 setup.md                                           |  11 +-
 16 files changed, 456 insertions(+), 143 deletions(-)

What does this mean?

If you have source files that require output and figures to be generated (e.g. R Markdown), then it is important to make sure the generated figures and output are reproducible.

This output provides a way for you to inspect the output in a diff-friendly manner so that it's easy to see the changes that occur due to new software versions or randomisation.

⏱️ Updated at 2024-05-05 11:30:26 +0000

[skanwal]

🌶️ 👍