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

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

8 Dec 2020F1000Research

Authors

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

Abstract

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.

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

Authors

Abstract

Members

PHILIPPE HUPE

ELODIE GIRARD

CHOUMOUSS KAMOUN

HENRI DE SOYRES

APOLLINE GALLOIS