Verify the user inputs are correct

[mfoll]

For parameters:

• sample_names
• do_plots
• all_sites

See here for example

[mfoll]

It would be good to also check that the input files exists (fasta, index and bed) and that the BAM folder also exists (see http://www.nextflow.io/docs/latest/script.html#check-file-attributes). I think that you can do something like:

assert params.fasta_ref.exists()

[mfoll]

values of 0 for map_qual and base_qualshould be valid (means no filter).

[mfoll]

It was not necessary a good idea for everything: some files might only be accessible during the execution of the processes (for example if you put the fasta ref on the scratch of the nodes of a cluster). We could either move the checks to later points (in the processes themselves) or add an option to prevent the checks, or even remove them?