Evolution of Nextflow command line interface

Nextflow CLI is quite flexible, however, there are some legacy problems hard to solve without re-engineering it.

Common problems are:

1. the lack of support list values
2. the mix of nextflow options pipeline parameters with
3. the use of the non-standard convention of options prefix i.e. -long-option instead of more --common --long-option
4. implicit type conversion can have nasty side-effects
5. double-notation (ie. --fooBar and --foo-bar) for pipeline params can create ambiguity and unexpected errors

The goal of this issue is to introduce a nextflow command line tool, named nf to address the above issue and keep backward compatibility with the existing command line whenever possible.

The following features should be supported

• use the GNU syntax conventions for command line options. Therefore - is only used for single char options and the prefix -- is used for options for two or more characters.
• Support list of values when an option is repeated more than once
• Implicit conversion only for basic types i.e. integer numbers and boolean values (true/false)
• Separate nextflow options from pipeline options using -- separate e.g. nextflow run <pipeline> --resume -- --foo --bar
• avoid double notation for pipeline parameters

See also https://github.com/nextflow-io/nextflow/issues/556