biogitflow: development workflow protocols for bioinformatics pipelines with git and GitLab

Nom de la revue
Choumouss Kamoun, Julien Roméjon, Henri de Soyres, Apolline Gallois, Elodie Girard, Philippe Hupé

The use of a bioinformatics pipeline as a tool to support diagnostic and theranostic decisions in the healthcare process requires the definition of detailed development workflow guidelines. Therefore, we implemented protocols that describe step-by-step all the command lines and actions that the developers have to follow. Our protocols capitalized on the two powerful and widely used tools git and GitLab, and are based on gitflow, a well-established workflow in the software engineering community. They address two use cases: a nominal mode to develop a new feature in the bioinformatics pipeline and a hotfix mode to correct a bug that occurred in the production environment. The protocols are available as a comprehensive documentation at and the main concepts, steps and principles are presented in this report.