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wjlim
by wjlim

search-pipelines

Search and filter nf-core bioinformatics pipelines using specific queries and pipeline names to streamline workflow selection and management.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pipelineNo
queryYes

Implementation Reference

  • 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
        };
      }
    }
  • 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
          };
        }
      }
    );
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Conciseness1/5

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Completeness1/5

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Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters1/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Tool has no description.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose1/5

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Tool has no description.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines1/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

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Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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