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Related Experiment Video

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Advanced Workflow for Taking High-Quality Increment Cores - New Techniques and Devices
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Watchdog 2.0: New developments for reusability, reproducibility, and workflow execution.

Michael Kluge1, Marie-Sophie Friedl1, Amrei L Menzel1

  • 1Institut für Informatik, Ludwig-Maximilians-Universität München, Amalienstr. 17, Munich 80333, Germany.

Gigascience
|June 20, 2020
PubMed
Summary
This summary is machine-generated.

Watchdog 2.0 enhances biological data analysis workflows with improved module creation, reusability, and documentation. This workflow management system ensures reproducible results and offers flexible execution modes for large-scale bioinformatics.

Keywords:
automated biological data analysisbioinformaticsnext-generation sequencingopen science toolsreproducibilityreusabilityworkflow management system

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Area of Science:

  • Bioinformatics and Computational Biology
  • Genomics and Proteomics Data Analysis
  • Scientific Workflow Management

Background:

  • High-throughput methods generate large biological datasets requiring complex, multi-step analyses.
  • Workflow management systems automate and standardize the execution of these large-scale data analysis pipelines.
  • Previous systems like Watchdog provided foundational capabilities for automated biological data analysis.

Purpose of the Study:

  • To introduce Watchdog 2.0, an advanced workflow management system.
  • To enhance module creation, reusability, documentation, and reproducibility in biological data analysis.
  • To provide new features for flexible and robust workflow execution.

Main Methods:

  • Development of a graphical user interface for semi-automatic module creation.
  • Implementation of sharing repositories for modules and workflows.
  • Standardized module documentation format for generating reference books.
  • Extensive logging of workflow execution, software versions, and support for package managers/containerization.
  • Introduction of two new execution modes: resuming interrupted workflows and detaching/reattaching to cluster execution.

Main Results:

  • Watchdog 2.0 offers improved module creation, reusability, and documentation capabilities.
  • Enhanced reproducibility through detailed logging and support for modern software management tools.
  • New execution modes allow for interrupted workflow resumption and flexible remote execution.
  • A standardized documentation format facilitates the creation of analysis protocols and method sections.

Conclusions:

  • Watchdog 2.0 provides significant advancements for large-scale bioinformatics analysis.
  • Its features, including module repositories and enhanced reproducibility, are not fully matched by competing systems.
  • The software, repositories, and documentation are freely available for scientific use.