nf-core MCP Server

Implementation Reference

• src/index.ts:69-91 (handler)

  The handler function reads the modules.json file from the specified pipeline directory, parses it, and returns the JSON content as text. Handles errors by returning an error message.

    async ({ pipeline }) => {
      try {
        const modulesPath = path.join(process.cwd(), pipeline, "modules.json");
        const modulesContent = await fs.readFile(modulesPath, 'utf-8');
        const modules = JSON.parse(modulesContent);
        
        return {
          content: [{ 
            type: "text", 
            text: JSON.stringify(modules, null, 2)
          }]
        };
      } catch (error) {
        return {
          content: [{ 
            type: "text", 
            text: `Error getting pipeline modules: ${error}`
          }],
          isError: true
        };
      }
    }
  );

• src/index.ts:66-68 (schema)

  Input schema validating the 'pipeline' parameter as a string using Zod.

  { 
    pipeline: z.string()
  },

• src/index.ts:64-92 (registration)

  Registers the 'get-pipeline-modules' tool with MCP server, including name, input schema, and handler function.

  server.tool(
    "get-pipeline-modules",
    { 
      pipeline: z.string()
    },
    async ({ pipeline }) => {
      try {
        const modulesPath = path.join(process.cwd(), pipeline, "modules.json");
        const modulesContent = await fs.readFile(modulesPath, 'utf-8');
        const modules = JSON.parse(modulesContent);
        
        return {
          content: [{ 
            type: "text", 
            text: JSON.stringify(modules, null, 2)
          }]
        };
      } catch (error) {
        return {
          content: [{ 
            type: "text", 
            text: `Error getting pipeline modules: ${error}`
          }],
          isError: true
        };
      }
    }
  );