Geniac: Automatic Configuration GENerator and Installer for nextflow pipelines.

Area of Science:

• Bioinformatics and Computational Biology
• Genomics and Proteomics
• Data Science in Life Sciences

Background:

• High-throughput biotechnological platforms generate massive datasets, necessitating efficient computational analysis.
• Standard bioinformatics pipelines face challenges in real-time data processing and timely delivery to end-users.
• Workflow management systems, packaging, and containerization offer solutions but require standardization.

Purpose of the Study:

• To propose a set of best practices for developing and deploying bioinformatics pipelines for production operations.
• To promote homogeneity in workflow implementation, ensuring usability, maintainability, interoperability, sustainability, portability, reproducibility, scalability, and efficiency.
• To introduce Geniac, a toolbox designed to harmonize development practices and automate pipeline deployment.

Main Methods:

• Leveraging Nextflow, Conda, Docker, Singularity, and the nf-core initiative.
• Developing coding guidelines for Nextflow bioinformatics pipelines.
• Implementing Geniac, a toolbox with technical documentation, a command-line interface with a linter, and an add-on for configuration and deployment automation.

Main Results:

• Geniac provides comprehensive guidelines for bioinformatics pipeline development.
• A linter within Geniac checks code adherence to established best practices.
• The toolbox automates the generation of configuration files and container builds for Nextflow pipelines.

Conclusions:

• Geniac facilitates the harmonization of development practices across diverse expert communities.
• The toolbox streamlines the deployment of bioinformatics pipelines for production environments.
• Implementing Geniac enhances the overall quality and efficiency of bioinformatics workflow management.