SnakeMaker A Preview of A User-Friendly Tool For Biomedical Data Processing

Biomedical data analysis often relies on complex computational steps, leading to pipelines that are challenging to reproduce and share. These scripts, while powerful, can be difficult to understand and modify, especially for researchers with limited programming experience. This lack of transparency deteriorates collaboration and impedes the verification of scientific findings. To address this, we introduce SnakeMaker, a novel tool that simplifies the creation of reproducible and shareable workflows using the Snakemake workflow management system. SnakeMaker parses a set of user-friendly configuration files that specify inputs, outputs, parameters, and shell commands (or custom Python functions), automatically generating a complete Snakemake workflow. This approach significantly reduces the complexity of workflow definition, while enhancing transparency and reproducibility. By enabling easier workflow creation, sharing, and execution, SnakeMaker aims to foster collaboration and improve the reliability of neuroimaging research. The tool's modular design also allows for the creation and sharing of specialized ”forks” tailored to specific analysis pipelines, promoting a community-driven approach to workflow development. SnakeMaker has the potential to be a valuable resource for the scientific community, facilitating robust and reproducible research practices.