Introduction

This documentation describes guidelines for the development workflow of a bioinformatics pipeline from software development to deployment in production. The guidelines capitalizes on the gitflow model.

We assume that the reader is familiar with git and GitLab. However, we provide a brief Git tutorial and GitLab tutorial.

The documentation consists of three main sections:

1. The section Development workflow first describes the general principles of the development workflow we implemented. The branching model is presented along with the different use cases.

2. The section Nominal procedure then describes the first use case to develop a new release of the bioinformatics pipeline:

   • The General overview introduces the different steps of the use case,

   • The Technical procedure details all the actions and command lines step-by-step,

   • The Graphical synopsis of the procedure summarizes the technical actions.

3. The section Hotfix procedure then describes the second use case to correct a critical bug that has occurred in the production environment:

   • The General overview introduces the different steps of the use case,

   • The Technical procedure details all the actions and command lines step-by-step,

   • The Graphical synopsis of the procedure summarizes the technical actions.

Prerequisite

All the protocols require that you have set up a GitLab repository as explained in the section Create a new project in Gitlab.

Useful resources

Useful resources for biogitflow are available here:

• biogitflow documentation

• biogitflow template

• source of the biogitflow documentation

Cite us

Kamoun C, Roméjon J, de Soyres H et al. biogitflow: development workflow protocols for bioinformatics pipelines with git and GitLab [version 3; peer review: 2 approved]. F1000Research 2021, 9:632 (https://doi.org/10.12688/f1000research.24714.3).