SnsWESAnalysisOutput class not compatible with other sns pipeline outputs

[stevekm]

Tried to implement sns RNA-Seq pipeline but the SnsWESAnalysisOutput class (from here) has issues with compatibility, due to validation and methods which rely on sns wes specific files.

Need to find a way to refactor so that we can use other types of pipelines

Need to fork the project, leave snsxt as-is, develop new framework that is not tied to sns wes as tightly?

Maybe deprecate many of the methods of analysis objects which are no longer used or needed, and instead implement them as methods of SnsTask objects. In this way, sns attributes will be tied to the individual sns pipelines and not to the analysis object as a whole

[stevekm]

working on new Analysis and Sample classes for this here
https://github.com/NYU-Molecular-Pathology/snsxt/blob/refactor-analysis-task-classes/snsxt/analysis.py

[stevekm]

need to offload the old analysis object's validate() method onto the task objects
need to offload qsub log validations to the job manager