biogitflow: development workflow protocols for bioinformatics pipelines with git and GitLab [version 1; peer review: 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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Veröffentlicht in: | F1000 research 2020, Vol.9, p.632 |
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Hauptverfasser: | , , , , , |
Format: | Artikel |
Sprache: | eng |
Online-Zugang: | Volltext |
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Zusammenfassung: | 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.24714.1 |