Chapter 1 Intro to workflow management

1.1 Workflow management and automation

“Ideally, the reproduction of your results is a one-button operation. And this is valuable not just for others, but also for yourself (or your future self). For example, if the primary data should change (and it often does), wouldn’t it be nice to have one command that re-runs everything?”

• Karl Broman

Workflow management software can coordinate the steps of your workflow (raw files > analyses > outputs). It’s more reliable than memorizing the order scripts are supposed to run in, or hoping humans follow your README file correctly. Some can coordinate multiple programs and file formats.

Graphic from Philip Jia Guo, 2012 p.5, CC BY-NC 3.0

Workflows can get complicated! So it helps to have tools to wrangle them and to make them understandable by a broad audience.