handle new schema structure in `nf-core pipelines create-params-file`

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 73.07692% with 7 lines in your changes missing coverage. Please review.

Project coverage is 75.84%. Comparing base (27659c5) to head (e57a096). Report is 5 commits behind head on dev.

Files with missing lines	Patch %	Lines
nf_core/pipelines/params_file.py	72.00%	7 Missing :warning:

Additional details and impacted files

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