Improve nextflow implementation

[pditommaso]

This commit improves the nextflow implementation in several aspects:

• use path instead of file in input/output declaration
• properly declares inputs instead of using params
• use publishDir to generate expected pipeline output files
• declare pipeline params at the top of the script
• remove help custom function to make uniform with other implementations

If you are happy with these changes, I can modify the script to make it DSL2 complaint.

Also, consider including in this repo the test dataset and the Dockerfile for the required tool dependency.

[pditommaso]

Nice, I'd to merge this PR and I'll create a new one for DSL2 syntax. 👍

[jonathangoeke]

Thanks again! Please create a new pull request for DSL2, that would be great!