case_list file, svs folder

[tdiprima]

Problem: Some parts of the pipeline read from a list of Case IDs. BUT phase 1 of the pipeline just looks in the data/svs folder to see which files are there, and runs the pipeline on those files; not on anything listed in case_list.txt.

Why is this a problem? Because if someone forgets to put their "new" svs file in the folder, they will run the pipeline and be puzzled as to why it's running on their "previous" slide.

Proposed Solutions: It would be good if a script was added to check case_list.txt versus what file(s) are in the svs folder, and alert the user if necessary.

OR just have the scripts read from either the text file OR the svs folder.