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wft4galaxy: a workflow testing tool for galaxy.

Marco Enrico Piras1, Luca Pireddu1, Gianluigi Zanetti1

  • 1Data Intensive Computing, CRS4 (Center of Advanced Studies, Research and Development in Sardinia), Pula 09010, Italy.

Bioinformatics (Oxford, England)
|October 17, 2017
PubMed
Summary
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Automated testing for Galaxy workflows is now possible with wft4galaxy, a new tool that simplifies continuous integration and ensures analysis correctness. This enhances the reliability of complex scientific computational procedures.

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Scientific Computing

Background:

  • Workflow managers like Galaxy are crucial for standardizing and automating complex scientific analyses.
  • Ensuring the correctness of these sophisticated workflows has been a significant challenge.
  • Existing methods lack a straightforward approach for automated testing of Galaxy workflows.

Purpose of the Study:

  • To introduce a novel tool, wft4galaxy, for the automated testing of Galaxy workflows.
  • To enable continuous integration practices in the development of scientific workflows.
  • To facilitate the prompt detection of defects in complex analysis pipelines.

Main Methods:

  • Development of wft4galaxy, a tool designed for automated testing of Galaxy workflows.

Related Experiment Videos

  • Implementation of easy installation options, including a standard Python program and a Docker container.
  • Integration of wft4galaxy into the workflow development lifecycle for continuous testing.

    • Main Results:

    • wft4galaxy provides a feasible solution for bringing automated testing to Galaxy workflows.
    • The tool supports continuous integration, leading to earlier defect detection.
    • Simplified installation via Python or Docker reduces the barrier to adoption.

    Conclusions:

    • Automated testing of Galaxy workflows is now achievable with wft4galaxy.
    • The tool enhances the reliability and correctness of scientific analysis pipelines.
    • wft4galaxy facilitates more robust and maintainable workflow development.