Simplifying the development of portable, scalable, and reproducible workflows

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Command-line software is vital in biology research but has inconsistent installation and execution processes.
• The Common Workflow Language (CWL) is a community standard designed to address these inconsistencies.
• CWL enables formal description of tool inputs, outputs, and execution, including containerization for portability.

Purpose of the Study:

• To explain key concepts of CWL and software containers for biology research.
• To introduce ToolJig, a web application for interactively creating CWL documents.
• To provide examples for using CWL in biological research and facilitate adoption.

Main Methods:

• Development of ToolJig, a web application for interactive CWL document creation.
• ToolJig validates user-provided information for completeness and adherence to CWL specifications.
• Generation of example CWL tools, workflows, and input-object files for execution via workflow engines.

Main Results:

• ToolJig enables researchers to create CWL documents without manual coding.
• The application ensures the validity and completeness of CWL specifications.
• Users can generate input-object files and obtain execution examples for CWL tools and workflows.

Conclusions:

• ToolJig lowers the barrier to entry for using CWL in biological research.
• Interactive creation and validation of CWL documents promote reproducible science.
• The availability of ToolJig and examples supports broader adoption of CWL in bioinformatics.