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

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 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 https://biogitflow.readthedocs.io and the main concepts, steps and principles are presented in this report.

Highlights

Any reports and responses or comments on the article can be found at the end of the article
The first one is the nominal mode (Figure 1) in which a new feature is implemented to improve the bioinformatics pipeline based on requirements and expectations from the end-users who operate it for their daily clinical practice
The biogitflow documentation provides all the technical details, on how to configure the remote repository in GitLab to develop a new bioinformatics pipeline, how to use git and GitLab depending on the roles and permissions during the time frame of the development workflow for both use cases

Summary

Introduction

Any reports and responses or comments on the article can be found at the end of the article. Compliance with the healthcare laboratory accreditation standards and regulations is required for the development and exploitation of the bioinformatics pipeline In this context, several authors (Hume et al, 2019; INCa, 2018; Matthijs et al, 2016; Roy et al, 2018) recommended in their guidelines that an appropriate code repository tool should be used to enforce version control. Several authors (Hume et al, 2019; INCa, 2018; Matthijs et al, 2016; Roy et al, 2018) recommended in their guidelines that an appropriate code repository tool should be used to enforce version control It ensures to track the different releases of the bioinformatics pipeline, their validation and the developers involved in their implementation. We implemented the set of protocols biogitflow (Kamoun et al, 2020)

Methods

Results

Discussion

Conclusion