biogitflow: development workflow protocols for bioinformatics pipelines with git and GitLab [version 2; peer review: 1 approved, 1 approved with reservations]

Authors :: Choumouss Kamoun
Julien Roméjon
Henri de Soyres
Apolline Gallois
Elodie Girard
Philippe Hupé
Author Affiliations :: <relatesTo>1</relatesTo>Institut Curie, Paris, F-75005, France<br /><relatesTo>2</relatesTo>U900, Inserm, Paris, F-75005, France<br /><relatesTo>3</relatesTo>PSL Research University, Paris, France<br /><relatesTo>4</relatesTo>Mines Paris Tech, Fontainebleau, F-77305, France<br /><relatesTo>5</relatesTo>UMR144, CNRS, Paris, F-75005, France
Source :: F1000Research. 9:632
Publication Year :: 2020
Publisher :: London, UK: F1000 Research Limited, 2020.
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.

Subjects :: Brief Report
Articles
development workflow
bioinformatics pipeline
quality management
healthcare

ISSN :: 20461402
Volume :: 9
Database :: F1000Research
Journal :: F1000Research
Notes :: Revised Amendments from Version 1 This version improves upon the main issues raised by the reviewer1. First, we have highlighted what was the targeted audience of these protocols and how they have been beneficial on our practices. Then, a detailed comparison between biogitflow and gitflow has been provided. We have also added the link of the biogitflow template and have described its features. Finally, a critical analysis of the usage and possible improvements of these protocols have been discussed., , [version 2; peer review: 1 approved, 1 approved with reservations]
Publication Type :: Academic Journal
Accession number :: edsfor.10.12688.f1000research.24714.2
Document Type :: brief-report
Full Text :: https://doi.org/10.12688/f1000research.24714.2

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