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Kamoun, Choumouss; Roméjon, Julien; de Soyres, Henri; Gallois, Apolline; Girard, Elodie; Hupé, Philippe
F1000 research, 01/2020, Letnik: 9Journal Article
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 two powerful and widely used tools: git and GitLab. 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 https://biogitflow.readthedocs.io and the main concepts, steps and principles are presented in this report.
