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NGS360

NGS360 MCP Server

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by NGS360

wes_run_workflow

Submit a workflow run to the WES service by specifying workflow URL, type, version, and optional parameters. Supports CWL/WDL workflows.

Instructions

Submit a new workflow run to the WES service.

Args: workflow_url: URL or relative path to the workflow definition (CWL/WDL) workflow_type: Workflow language type (e.g., "CWL", "WDL") workflow_type_version: Version of the workflow language (e.g., "v1.0") workflow_params: Input parameters for the workflow (JSON object) workflow_engine: Workflow engine to use (e.g., "cromwell", "toil") workflow_engine_version: Version of the workflow engine workflow_engine_parameters: Additional engine-specific parameters tags: Arbitrary key-value tags for the run

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
tagsNo
workflow_urlYes
workflow_typeYes
workflow_engineNo
workflow_paramsNo
workflow_type_versionYes
workflow_engine_versionNo
workflow_engine_parametersNo
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations are provided, so the description must fully disclose behavioral traits. It only states 'submit' without explaining side effects (e.g., long-running process), success/failure behavior, authentication needs, or impact on other resources.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is concise: a single-purpose sentence at the start followed by a parameter list. It is front-loaded and avoids unnecessary words, though the parameter descriptions could be more streamlined.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given 8 parameters, no output schema, and no annotations, the description is insufficient. It omits details on asynchronous execution, tracking, return values, and error handling. For a WES submission tool, more context is needed.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, so the description must compensate. It provides brief explanations for each parameter (e.g., 'URL or relative path to the workflow definition (CWL/WDL)', 'Workflow language type (e.g., "CWL", "WDL")'). These add some value but are minimal, lacking constraints or examples for optional parameters.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states 'Submit a new workflow run to the WES service' using a specific verb ('submit') and resource ('workflow run'). It distinguishes from sibling tools like wes_cancel_run and wes_get_run_log by focusing on submission.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description offers no guidance on when to use this tool versus alternatives (e.g., submit_job, submit_demux_job). It does not mention prerequisites, when not to use it, or how it fits in the broader workflow lifecycle.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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