updated: 2022-09-30
#tools/snakemake
One day at a dinner at a conference, a person next to me saying
"Presentation is something like---Everyone understands at the beginning. But then the audience gets confused, the chair gets confused, and even the speaker gets confused about what he is talking about."
Although I forgot who said this, this phrase sticks with me because I had such an experience (maybe he was talking about me).
The same applies to experiments. At the beginning of a research project, we often start with some preliminary experiments which can be small enough to be fitted into a notebook. Everyone would understand your notebook. As the experiment gets larger in scale, your collaborators get confused, your boss gets confused, and eventually, you get confused about what you are doing.
Experiments are repetitive. We run dozens of experiments daily with slightly different configurations across different datasets. The design of the experiments is often repeatedly changed during the course of a project. Making the workflow in order requires enormous effort and is time-consuming. That's where Snakemake comes in.