Unify the way NGS workflows output is set up

Some workflows allow to specify an output directory by selecting one of the values:

• Custom
• Input file - this value is selected by default!
• Workflow

And other workflows output the data into a common workflow_output directory. This doesn't correspond to the first way and creates a mess.

Also, it is not clear how to set up a custom directory in the wizard when "Custom" value is set up.