After discussion in nextflow-io/nextflow#866 we have decided not to use the JSON Schema hosted on the nf-core website. Instead, we will use the regular JSON Schema format for each pipeline.

The nf-core launch code needs updating to reflect this.

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Started in #591

Still to do:

• Fix (? for help) in booleans
• Make -a flag do what it is supposed to do
• Use defaults from nextflow config instead of schema? (warn if different from schema)
• When pulling, get latest release or if no release then default branch.
• Test with non-nf-core pipelines
• Description and help text for groups
• Check python tests
• Check that importing a params file at launch time works
• Grep main.nf (and other files?) for params.XX text that nextflow config has missed
• Update documentation
• Update changelog

Long term:

• Link to the website for using a GUI to prepare parameters, instead of the CLI (if desired)