2451 schema build update defaults

[awgymer]

Fixes #2451

Implemented the option (via questionary) to update the schema defaults where the default in the pipeline appears to have changed.

A similar but reverse issue is found in #1954
Perhaps there is some scope here to issue warnings to assist in that?

Also implemented some additional code to ensure that non-zero False-y defaults are no longer written by python (current behaviour relies on web-builder to handle this but that is not used by all)

Considerations:

• Should determine some suitable tests for this new behaviour
• Do we need to allow params to be excluded (in e.g. .nf-core.yml) so that known divergent defaults can be safely ignored?

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

Attention: 15 lines in your changes are missing coverage. Please review.

Comparison is base (960bff5) 74.98% compared to head (2c9ccec) 74.93%.
Report is 4 commits behind head on dev.

Files	Patch %	Lines
nf_core/schema.py	51.61%	15 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev    #2479      +/-   ##
==========================================
- Coverage   74.98%   74.93%   -0.06%     
==========================================
  Files          85       85              
  Lines        9327     9356      +29     
==========================================
+ Hits         6994     7011      +17     
- Misses       2333     2345      +12     

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[mirpedrol]

LGTM thank you!!
But the new mypy linting is failing, so we should have a look before merging :)

[mashehu]

LGTM thank you!! But the new mypy linting is failing, so we should have a look before merging :)

These are all not yet typed files, so it is a case related to this #2480 and can be ignored, I think

[mirpedrol]

I see! OK for me to merge then

[mirpedrol]

@nf-core-bot fix linting please!