Fix rich codex images

[mirpedrol]

Add repository_type in .nf-core.yml files from rich codex.

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

[codecov]

Codecov Report

Merging #2188 (c569daa) into dev (fc7bf54) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##              dev    #2188   +/-   ##
=======================================
  Coverage   71.57%   71.57%           
=======================================
  Files          77       77           
  Lines        8369     8369           
=======================================
  Hits         5990     5990           
  Misses       2379     2379           

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[mashehu]

Can this error occur also for normal users? if so we should catch it and print a nicer message.

[mirpedrol]

We ask on a terminal prompt to automatically add the value to .nf-core.yml 🙂