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

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 deve...

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Bibliographic Details
Published in:F1000 research Vol. 9; p. 632
Main Authors: Kamoun, Choumouss, Roméjon, Julien, de Soyres, Henri, Gallois, Apolline, Girard, Elodie, Hupé, Philippe
Format: Journal Article
Language:English
Published: 01.01.2020
Subjects:
bioinformatics pipeline
development workflow
quality management
healthcare
ISSN:2046-1402, 2046-1402
Online Access:Get full text
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Summary: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.
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ISSN:2046-1402
2046-1402
DOI:10.12688/f1000research.24714.2