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Related Experiment Video

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Compi: a framework for portable and reproducible pipelines.

Hugo López-Fernández1,2,3, Osvaldo Graña-Castro4, Alba Nogueira-Rodríguez1,2,3

  • 1ESEI: Escuela Superior de Ingeniería Informática, University of Vigo, Ourense, Galicia, Spain.

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|July 9, 2021
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Summary
This summary is machine-generated.

Compi simplifies research by enabling easy creation, packaging, and sharing of pipeline applications. This framework offers researchers workflow engine benefits with shell script simplicity, avoiding new programming languages.

Keywords:
Application development frameworkComputational pipelinesWorkflow management systems

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Software Engineering

Background:

  • Traditional workflow engines often require learning new programming languages, posing a barrier for researchers.
  • Developing and distributing pipeline-based applications can be complex and time-consuming.

Purpose of the Study:

  • Introduce Compi, an application framework designed to simplify the development, packaging, and distribution of end-user, pipeline-based applications.
  • Enable researchers to leverage workflow engine features while maintaining the simplicity of shell scripts.

Main Methods:

  • Compi automatically generates command-line interfaces from pipeline parameter definitions.
  • Compi-DK facilitates packaging pipeline applications and dependencies into version-control-friendly Docker images.
  • Compi Hub provides a public repository for discovering, browsing, and reusing Compi pipelines.

Main Results:

  • Compi addresses user interface generation, application packaging, and distribution through a public repository.
  • The framework integrates features like automatic job scheduling and logging.
  • Compi pipelines are designed for simplicity and readability, similar to shell scripts.

Conclusions:

  • Compi offers a novel solution for researchers seeking the power of workflow engines with the ease of shell scripting.
  • The framework promotes code reuse and simplifies the deployment of bioinformatics pipelines.
  • Compi enhances accessibility to advanced computational tools for a broader research community.