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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
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biogitflow: development workflow protocols for bioinformatics pipelines with git and GitLab.

Choumouss Kamoun1,2,3,4, Julien Roméjon1,2,3,4, Henri de Soyres1,2,3,4

  • 1Institut Curie, Paris, F-75005, France.

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|March 22, 2021
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Summary
This summary is machine-generated.

This study introduces git and GitLab-based protocols for developing bioinformatics pipelines, ensuring reproducible workflows for diagnostic and theranostic decision support. These guidelines streamline feature development and bug fixing in healthcare bioinformatics.

Keywords:
bioinformatics pipelinedevelopment workflowhealthcarequality management

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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.