Trivial It is not comfortable for a user each time to open the Workflow Designer, choose an input file in a workflow, run it, etc.
It would be nice to be able to launch the workflow e.g. from the Sequence View or from the Alignment Editor.
Therefore a new functionality should be added to allow a user to e.g. add a new button (maybe on the toolbar) and associate this button with a particular workflow.
Of course, it should be possible to add more than one such custom buttons 
So the workflow is run with the active sequence (or sequences) or alignment as the input file.
The output file should be optionally added to the project.