Use common interface for exposed workflows of modules in the same category

[emi80]

Hi all, as discussed during today's meeting, it might be good to use common interfaces for exposed workflows of modules belonging to the same category (e.g. alignment).

For example, for a given module in the alignment category the interface could include INDEX, MAP and ALIGN. So, for the current STAR module, one would rename the exposed workflows as follows:

• STAR_INDEX -> INDEX
• STAR_INDEX_NOANNO -> move to INDEX and use some logic or an optional input to use the same workflow with/without theannotation (if not really possible include INDEX_NOANNO to the interface)
• STAR_MAP -> MAP
• STAR_ALL -> ALIGN

Thoughts and comments are welcome!

Cheers

[lucacozzuto]

Hi Emilio! Good idea. I'll work on it.

L

[lucacozzuto]

I changed the names. I don't put the choice of indexing with or without the annotation at the level of INDEX but later on (ALL)