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NGS360

NGS360 MCP Server

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by NGS360

submit_pipeline_job

Submit a pipeline job to AWS Batch for a bioinformatics project by specifying project ID, action, platform, and workflow type. Optionally set export reference and auto-release flag.

Instructions

Submit a pipeline job to AWS Batch for a project.

Args: project_id: The project identifier action: Pipeline action (create-project or export-project-results) platform: Platform name (Arvados or SevenBridges) project_type: Pipeline workflow type (e.g., RNA-Seq, WGS) reference: Export reference (required for export action) auto_release: Auto-release flag for export action

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
actionYes
platformYes
referenceNo
project_idYes
auto_releaseNo
project_typeYes
Behavior2/5

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

With no annotations, the description should disclose behavioral traits. It only states the action (submit to AWS Batch) but fails to mention side effects, blocking behavior, authentication needs, or error handling.

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 a concise list of parameters with brief explanations. It is well-structured and front-loaded with the main purpose. Could be slightly more compact but overall efficient.

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

Completeness3/5

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

Given no output schema and 6 parameters, the description covers purpose and parameter meanings but lacks context on return values, job tracking, or error conditions. Adequate but not fully complete.

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

Parameters4/5

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

Despite 0% schema description coverage, the description adds value by explaining allowed values for action (create-project or export-project-results) and clarifying that reference is required for export. This goes beyond the schema's property names.

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 the verb 'Submit' and the resource 'pipeline job to AWS Batch for a project', distinguishing it from sibling tools like submit_job or submit_demux_job.

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?

No guidance on when to use this tool versus alternatives such as submit_job or other pipeline-related tools. No prerequisites or exclusions mentioned.

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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