Add defaults configuration settings

[pditommaso]

This PR aims to make default settings configurable via the nextflow configuration file.

The primary goal is to allow the control the defaults of publishDir directive. It can be extend to cover the settings of almost any other configuration attribute.

Solves #4186

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[bentsherman]

I don't see the point in doing this. We are planning to replace publishDir with the workflow output DSL, which I have shown can provide a simple way to provide publish defaults without so much repetition (nf-core/fetchngs#275). And when you put aside publishDir, there is no other process directive that would benefit from this sort of defaults scope.