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seqera-automation

Automate Seqera tasks via Rube MCP (Composio). Always search tools first for current schemas.

Author

@ComposioHQ

Category

Development Tools

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seqera-automation - Seqera Task Automation Guide

Skills Overview

seqera-automation is a Claude skill for automating Seqera workflows via Composio’s Rube MCP. It helps users intelligently discover Seqera tools, manage connection status, and execute automation tasks in bulk.

Use Cases

  • Bioinformatics workflow automation: Automatically run Nextflow workflows, batch-process sequencing data, and schedule pipeline tasks—without manual interaction with the Seqera platform.

  • Enterprise-scale batch task management: Handle multiple Seqera tasks at the same time, batch-create workflows, and centrally monitor and manage all run statuses to improve team collaboration efficiency.

  • Fast tool integration and development: Use Rube MCP to dynamically discover available Seqera tools, fetch the latest API schemas, and simplify the integration development process.

    • Core Capabilities

  • Intelligent tool discovery: Automatically search for currently available Seqera tools via RUBE_SEARCH_TOOLS, retrieve the latest tool schema and recommended execution plan, and avoid outdated API calls caused by hardcoding.

  • Connection status management: Use RUBE_MANAGE_CONNECTIONS to check Seqera connection status in real time. One-click completes identity/authentication configuration to ensure all automation tasks run under active connections.

  • Batch task execution: Use RUBE_MULTI_EXECUTE_TOOL to execute multiple Seqera operations in parallel. Supports session reuse, memory management, and pagination handling—ideal for large-scale workflow batch processing.

    • Common Questions

    What prerequisites does seqera-automation require?

    Before use, ensure: 1) Add the Rube MCP server to your client configuration (https://rube.app/mcp), no API key required; 2) Confirm that the RUBE_SEARCH_TOOLS tool is available; 3) Establish an active Seqera connection via RUBE_MANAGE_CONNECTIONS. It’s recommended to complete these steps before running any workflows.

    Why call RUBE_SEARCH_TOOLS before every execution?

    Seqera tool schemas in Composio are updated frequently. Hardcoding tool names and parameters is prone to errors. RUBE_SEARCH_TOOLS retrieves the latest API schemas, recommended execution plans, and known pitfalls—key to keeping automation tasks running reliably.

    How does seqera-automation differ from directly calling the Seqera API?

    seqera-automation provides an abstraction layer via Rube MCP: it automatically handles tool discovery, connection management, and bulk execution—so you don’t need to write API-calling code manually. It also provides session management and error handling, making it easy to build automation workflows quickly in Claude conversations. Direct API calls require more development effort and ongoing maintenance.

    How do I handle pagination for a large number of Seqera tasks?

    In the responses from RUBE_MULTI_EXECUTE_TOOL or RUBE_REMOTE_WORKBENCH, check pagination tokens. If they exist, continue requesting the next page of data until you receive the complete results. This is the recommended approach for handling large workflow lists or task history.

    How do I handle connection failures?

    Call RUBE_MANAGE_CONNECTIONS to check the connection status. If it shows a non-ACTIVE state, the skill returns an authentication link. After completing authentication, check the status again and execute the workflow only once the connection is confirmed restored. It’s recommended to add connection status checking logic in your automation scripts.