Split README to separate md documents into split_mds folder

[karegapauline]

PR checklist

• [ ] This comment contains a description of changes (with reason)
• [ ] CHANGELOG.md is updated
• [ ] If you've fixed a bug or added code that should be tested, add tests!
• [ ] Documentation in docs is updated

[github-actions[bot]]

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• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

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Hi @karegapauline,

It looks like this pull-request is has been made against the karegapauline/tools master branch. The master branch on nf-core repositories should always contain code from the latest release. Because of this, PRs to master are only allowed if they come from the karegapauline/tools dev branch.

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[codecov[bot]]

Codecov Report

Merging #1458 (c9e8d13) into dev (3abb7ef) will not change coverage. The diff coverage is n/a.

@@           Coverage Diff           @@
##              dev    #1458   +/-   ##
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  Coverage   64.87%   64.87%           
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  Files          52       52           
  Lines        6055     6055           
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  Hits         3928     3928           
  Misses       2127     2127           

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[ewels]

Great! Small thing from a first glance - please use all lower-caps for the filenames, as these will be used for the URLs.

[mashehu]

I like the idea with the subdirectories for schema, modules, etc., but I would propose to have then all files inside a directory called markdown, so the don't get mixed up with the two other directories.

[ewels]

Ah I forgot we already have api there, ok yeah - docs/markdown is good then 👍🏻

[ewels]

@karegapauline I just fixed the merge conflicts and then ran the new linting - please make sure you pull these changes before making any more edits..

[ewels]

Getting better, thanks for these updates!

One more thing: For the subcommands that have been broken into pages, could we have directories named after the subcommands?

So docs/markdown/modules/creating_new_modules.md for example.

Just to make it a little easier to navigate the docs.

[ewels]

Needs significant updates now and will probably be approached slightly differently with the website rewrite. Closing for now, can reopen closer to the time if the final implementation looks like it will use the same syntax 👍🏻