ToolJig

ToolJig generates Common Workflow Language (CWL) tool and workflow descriptions to enable portable, reproducible computational analyses.

Key Features:

• CWL document creation: Creates Common Workflow Language (CWL) tool and workflow description files.
• Validation and completeness assurance: Validates CWL documents for adherence to CWL specifications to ensure completeness and correctness.
• Portability and scalability: Produces workflows that can be executed on personal workstations, high-performance clusters, and cloud platforms.
• Support for software containers: Includes instructions for executing tools within software containers.
• Workflow dependency management: Describes dependencies among tools and links outputs from one tool to inputs of another.
• Input-object file creation: Generates input-object files that store invocation-specific values for tools and workflows.

Scientific Applications:

• Genomics: Enables creation of portable pipelines for batch processing large genomics and sequencing datasets to support reproducible analyses.
• Biological research workflows: Supports multi-step analytical workflows that require linking outputs and inputs across tools for diverse biological studies.

Methodology:

Validates CWL documents against CWL specifications and generates CWL tool and workflow descriptions and input-object files, with support for embedding container execution instructions and linking tool outputs to inputs.