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Good practices in bioinformatic or computational biology projects.

Bioinformatic or computational biology projects need to follow the same practices as lab projects and notebooks, with organized data, documented steps, the project structured for reproducibility, and the consistent code style.

Project Organization

It is generally a good idea to store all of the files relevant to one project under a common root directory. And organizing the files that make up a project in a logical and consistent directory structure will help you and others keep track of them.

The recommendations are drawn from:

Wilson, Greg, et al. “Good enough practices in scientific computing.” PLoS computational biology 13.6 (2017): e1005510.

Code style

Write code in a consistent style will make it easier to maintain, and easier for collaborators to understand. Code is more often read than written, and code style can also have a great impact on the readability of your code

The style guides here are fundamentally opinionated, but not too opinionated. And many decisions are arbitrary, any suggestions are welcome.

The bash is derived from Google’s shell style guide; python code style is derived from Google’s python style guide and PEP 8 style guide for python; the R code style is derived from Tidyverse Style Guide; and WDL style is derived from BioWDL style.

If you’re modifying existing files, you should follow the style that’s already in the files.

Do what Romans do in Rome.