nf-core MCP Server

Implementation Reference

• src/index.ts:100-144 (handler)

  The main handler function for the 'search-pipelines' tool. It recursively searches files in the specified pipeline directory (or root) for the query string, targeting .nf, .config, and .json files, and returns a JSON list of matching file paths.

  async ({ query, pipeline }) => {
    try {
      const searchPath = pipeline ? path.join(process.cwd(), pipeline) : process.cwd();
      const results: string[] = [];
      
      async function searchDir(dir: string) {
        const entries = await fs.readdir(dir, { withFileTypes: true });
        for (const entry of entries) {
          const fullPath = path.join(dir, entry.name);
          if (entry.isDirectory() && !entry.name.startsWith('.')) {
            await searchDir(fullPath);
          } else if (entry.isFile() && 
                    (entry.name.endsWith('.nf') || 
                     entry.name.endsWith('.config') || 
                     entry.name.endsWith('.json'))) {
            try {
              const content = await fs.readFile(fullPath, 'utf-8');
              if (content.includes(query)) {
                results.push(fullPath);
              }
            } catch (err) {
              console.error(`Error reading ${fullPath}: ${err}`);
            }
          }
        }
      }
      
      await searchDir(searchPath);
      
      return {
        content: [{ 
          type: "text", 
          text: JSON.stringify(results, null, 2)
        }]
      };
    } catch (error) {
      return {
        content: [{ 
          type: "text", 
          text: `Error searching pipelines: ${error}`
        }],
        isError: true
      };
    }
  }

• src/index.ts:96-99 (schema)

  Zod schema for the tool inputs: 'query' (required string to search for) and 'pipeline' (optional string specifying the pipeline directory).

  { 
    query: z.string(),
    pipeline: z.string().optional()
  },

• src/index.ts:94-145 (registration)

  Registration of the 'search-pipelines' tool on the MCP server using server.tool(name, schema, handler).

  server.tool(
    "search-pipelines",
    { 
      query: z.string(),
      pipeline: z.string().optional()
    },
    async ({ query, pipeline }) => {
      try {
        const searchPath = pipeline ? path.join(process.cwd(), pipeline) : process.cwd();
        const results: string[] = [];
        
        async function searchDir(dir: string) {
          const entries = await fs.readdir(dir, { withFileTypes: true });
          for (const entry of entries) {
            const fullPath = path.join(dir, entry.name);
            if (entry.isDirectory() && !entry.name.startsWith('.')) {
              await searchDir(fullPath);
            } else if (entry.isFile() && 
                      (entry.name.endsWith('.nf') || 
                       entry.name.endsWith('.config') || 
                       entry.name.endsWith('.json'))) {
              try {
                const content = await fs.readFile(fullPath, 'utf-8');
                if (content.includes(query)) {
                  results.push(fullPath);
                }
              } catch (err) {
                console.error(`Error reading ${fullPath}: ${err}`);
              }
            }
          }
        }
        
        await searchDir(searchPath);
        
        return {
          content: [{ 
            type: "text", 
            text: JSON.stringify(results, null, 2)
          }]
        };
      } catch (error) {
        return {
          content: [{ 
            type: "text", 
            text: `Error searching pipelines: ${error}`
          }],
          isError: true
        };
      }
    }
  );