biogitflow: development workflow protocols for bioinformatics pipelines with git and GitLab.

Area of Science:

• Bioinformatics
• Software Engineering
• Computational Biology
• Health Informatics

Background:

• Bioinformatics pipelines are crucial for diagnostic and theranostic decisions in healthcare.
• A standardized development workflow is essential for reliable and reproducible bioinformatics tools.
• Existing software engineering practices can be adapted to improve bioinformatics pipeline development.

Purpose of the Study:

• To define detailed development workflow guidelines for bioinformatics pipelines.
• To implement protocols supporting diagnostic and theranostic decision-making processes.
• To provide a reproducible framework for bioinformatics software development.

Main Methods:

• Implementation of step-by-step protocols using git and GitLab.
• Adoption of the gitflow branching model for structured development.
• Definition of protocols for nominal feature development and hotfix bug correction.

Main Results:

• Developed comprehensive protocols for bioinformatics pipeline development.
• Established clear guidelines for command lines and developer actions.
• Successfully addressed use cases for new feature integration and production bug fixes.

Conclusions:

• The implemented protocols enhance the reliability and reproducibility of bioinformatics pipelines.
• Git-based workflows facilitate efficient development and maintenance of healthcare bioinformatics tools.
• The documented protocols serve as a valuable resource for bioinformatics developers.