Bio-OS MCP Server

Example Use Cases

• 1

  Submit, monitor, and manage bioinformatics workflows (WDL/Cromwell) programmatically via the MCP protocol.

• 2

  Validate WDL scripts and generate input file templates to ensure correct workflow execution.

• 3

  Build Docker images, check build status, and retrieve build logs for workflow runtime containers, with support for local and cloud development environments.

Description

Bio-OS MCP Server exposes tools to submit and monitor WDL/Cromwell workflows, upload and validate WDL scripts, generate WDL input templates, and manage Docker image builds and logs. It is designed to integrate with the CLINE VSCode extension or run in a cloud Code Server environment for seamless development and execution. The server streamlines WDL development, runtime configuration, and container management to support reproducible bioinformatics workflows and CI-like image builds.