Project templates provide some standardized way to organize files. Our lab uses a template that is based off the Noble 2009 Paper, “A Quick Guide to Organizing Computational Biology Projects”. I’ve created a simple shell script that automatically generates this folder structure here, and there’s an rr-init project by the Reproducible Science Curriculum folks.
The structure we have in our lab looks like this:
project | |- data # raw and primary data, are not changed once created | | | |- project_data # subfolder that links to an encrypted data storage container | | | | | |- original # raw data, will not be altered | | |- working # intermediate datasets from src code | + +- final # datasets used in analysis | |- src / # any programmatic code | |- user1 # user1 assigned to the project | +- user2 # user2 assigned to the project | |- output # all output and results from workflows and analyses | |- figures/ # graphs, likely designated for manuscript figures | |- pictures/ # diagrams, images, and other non-graph graphics | +- analysis/ # generated reports for (e.