Check params for core nextflow flags

[ewels]

Literally everyone gets caught out with the classic nextflow gotcha of - or -- at some point. Using one hyphen for a param immediately exits with an error as it's not a recognised nextflow option. However, using two hyphens for a core nextflow option runs silently as it is a valid param.

What we could do to help people with this is to maintain a list of core nextflow flags in the template / pipeline, and just check that we don't have any params set with the same name. If we do, we exit immediately at the start of the pipeline with an error and link to some documentation to explain.

Phil

[ewels]

Implemented in #852