nf-core MCP Server

Implementation Reference

• src/index.ts:23-60 (handler)

  The handler function for the 'list-pipelines' tool. It lists hardcoded nf-core pipelines ('rnaseq', 'sarek', 'modules', 'tools') and for each checks if nextflow.config exists, returning details including whether config is present.

  async () => {
    try {
      const pipelines = ['rnaseq', 'sarek', 'modules', 'tools'];
      const pipelineDetails = await Promise.all(
        pipelines.map(async (name) => {
          const configPath = path.join(process.cwd(), name, "nextflow.config");
          try {
            const config = await fs.readFile(configPath, 'utf-8');
            return {
              name,
              hasConfig: true,
              configPath
            };
          } catch {
            return {
              name,
              hasConfig: false
            };
          }
        })
      );
      
      return {
        content: [{ 
          type: "text", 
          text: JSON.stringify(pipelineDetails, null, 2)
        }]
      };
    } catch (error) {
      return {
        content: [{ 
          type: "text", 
          text: `Error listing pipelines: ${error}`
        }],
        isError: true
      };
    }
  }

• src/index.ts:20-61 (registration)

  Registration of the 'list-pipelines' tool using server.tool(), with empty input schema and the handler function.

  server.tool(
    "list-pipelines",
    {},
    async () => {
      try {
        const pipelines = ['rnaseq', 'sarek', 'modules', 'tools'];
        const pipelineDetails = await Promise.all(
          pipelines.map(async (name) => {
            const configPath = path.join(process.cwd(), name, "nextflow.config");
            try {
              const config = await fs.readFile(configPath, 'utf-8');
              return {
                name,
                hasConfig: true,
                configPath
              };
            } catch {
              return {
                name,
                hasConfig: false
              };
            }
          })
        );
        
        return {
          content: [{ 
            type: "text", 
            text: JSON.stringify(pipelineDetails, null, 2)
          }]
        };
      } catch (error) {
        return {
          content: [{ 
            type: "text", 
            text: `Error listing pipelines: ${error}`
          }],
          isError: true
        };
      }
    }
  );

• src/index.ts:22-22 (schema)

  Empty input schema for the 'list-pipelines' tool (no parameters required).

  {},