update documentation about the configuration in either config or samplesheet

[fmalmeida]

The pipeline now has a few configuration parameters that can be set globally to all samples at once (when set via the CLI or config file), or specifically to a single sample (when passed inside the samplesheet).

Although a few cases of them are documented in the manual, others are not.

So we need to revise the documentation to make sure all these parameters are properly described in the manual and not only inside the config file.

Also revise the help message.

[fmalmeida]

Fixed!