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In the rapidly evolving landscape of computational biology and bioinformatics, the demand for robust workflow systems and pipelines has increased. Despite numerous advances in methodologies and technologies, ensuring reproducibility remains a concern. A few years ago, we introduced SEquence DAtaset builder (SEDA), an open-source application tailored for processing DNA and protein sequences in FASTA files. With a user-friendly graphical interface (GUI) and a newly introduced command-line interface (CLI) in version 1.6.0, SEDA is now adaptable to different bioinformatics requirements, including complex workflows. The “SEDA pipelines with Compi” framework presented in this work is built around the principles of convention over configuration (CoC), streamlining SEDA-based pipeline development by minimizing explicit coding requirements and enforcing standardized conventions. This approach not only reduces the workload for developers but also ensures consistency and ease of collaboration across projects. By leveraging Compi and CoC, our framework simplifies the creation of pipelines centered on SEDA commands. We demonstrate the effectiveness of our framework in simplifying pipeline development and enhancing reproducibility through three distinct use cases.

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Streamlining SEDA Pipelines with Compi: The Power of Convention over Configuration

  • 会议论文

  • 发表日期：

    2025年

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  • Daniel Pérez-Rodríguez,
  • Miguel Reboiro-Jato,
  • Cristina P. Vieira,
  • Jorge Vieira,
  • Hugo López-Fernández

摘要

In the rapidly evolving landscape of computational biology and bioinformatics, the demand for robust workflow systems and pipelines has increased. Despite numerous advances in methodologies and technologies, ensuring reproducibility remains a concern. A few years ago, we introduced SEquence DAtaset builder (SEDA), an open-source application tailored for processing DNA and protein sequences in FASTA files. With a user-friendly graphical interface (GUI) and a newly introduced command-line interface (CLI) in version 1.6.0, SEDA is now adaptable to different bioinformatics requirements, including complex workflows. The “SEDA pipelines with Compi” framework presented in this work is built around the principles of convention over configuration (CoC), streamlining SEDA-based pipeline development by minimizing explicit coding requirements and enforcing standardized conventions. This approach not only reduces the workload for developers but also ensures consistency and ease of collaboration across projects. By leveraging Compi and CoC, our framework simplifies the creation of pipelines centered on SEDA commands. We demonstrate the effectiveness of our framework in simplifying pipeline development and enhancing reproducibility through three distinct use cases.