Bioinformatics Project Organization

Set up a computational-biology project so a stranger can understand what was done and why, and so every analysis can be rerun end-to-end from a script. Apply this when creating, restructuring, or reproducibility-hardening any genomics, metagenomics, sequencing, or computational-biology project — and when running any single analysis command that should be reproducible.

Two assumptions drive every rule below (Noble 2009): a stranger must be able to reconstruct the analysis from the files alone, and everything will be rerun — with new data, new parameters, or a fixed bug — so build each experiment to re-execute from a script, never from memory.

Instructions

New project startup workflow

Before creating directories or running the first command, turn the project into a small written contract: