---

name: ast-grep description: > Structural code search and refactoring using AST patterns. Use when searching for code patterns (not text), finding deprecated patterns, or systematic refactoring. Supports Nextflow, JavaScript, Python, and more. license: MIT metadata: version: "1.0.0" author: "Edmund Miller"

ast-grep Skill

ast-grep is a structural code search and rewriting tool. Use it when you need to find or modify code based on its AST structure rather than text patterns.

When to Use ast-grep

Use ast-grep when:

• Searching for code patterns (function calls, imports, specific constructs)
• Refactoring code systematically
• Finding deprecated patterns or anti-patterns
• The pattern involves code structure, not just text

Use grep/ripgrep when:

• Searching for literal strings, comments, or documentation
• Simple text matching is sufficient

Quick Reference

Quick Start

Simple Pattern Search

Copy# Find all console.log calls
ast-grep run --pattern 'console.log($$$ARGS)' --lang js

# Find Channel.from() calls in Nextflow
ast-grep run --pattern 'Channel.from(___)' --lang nextflow

Using Rules for Complex Patterns

Copy# Scan with a rule file
ast-grep scan --rule path/to/rule.yaml

# Quick inline rule test
ast-grep scan --inline-rules '
id: test-rule
language: javascript
rule:
  pattern: console.log($$$ARGS)
'

Debugging Patterns

Copy# See AST structure of code
ast-grep run --pattern '$$$' --debug-query=ast path/to/file.js

# See how pattern matches
ast-grep run --pattern 'your_pattern' --debug-query=pattern path/to/file.js

Core Concepts

Metavariables

Note: In Nextflow, use _ instead of $ for metavariables (configured via expandoChar in sgconfig.yml).

Rule Structure

Copyid: rule-name
language: javascript  # or nextflow, python, etc.
severity: warning     # error, warning, hint, off
message: "Human-readable message"
note: |
  Additional context and fix suggestions
rule:
  pattern: code_pattern_here

Workflow for Writing Rules

1. Understand the query - What code pattern are you looking for?
2. Create example code - Write a small file with the pattern
3. Inspect the AST - Use --debug-query=ast to see structure
4. Write initial pattern - Start simple, use metavariables
5. Test and refine - Use --debug-query=pattern to debug matches
6. Add constraints - Use relational rules (inside, has) as needed

Common Patterns

Match function with specific content

Copyrule:
  all:
    - pattern: function $NAME($$$PARAMS) { $$$ }
    - has:
        pattern: console.log($$$)
        stopBy: end

Match code inside a context

Copyrule:
  all:
    - pattern: await $PROMISE
    - inside:
        kind: try_statement
        stopBy: end

Match missing pattern (lint for absence)

Copyrule:
  all:
    - pattern: function $NAME($$$) { $$$ }
    - not:
        has:
          pattern: return $$$
          stopBy: end

Key Principles

1. Always use stopBy: end for relational rules (inside, has, precedes, follows) to search the full subtree
2. Start simple - Get a basic pattern working before adding complexity
3. Escape $ in shell - Use \$VAR or single quotes when running from bash
4. Use all for order - When metavariables depend on each other, all processes rules in order

Integration Notes

OpenCode Tools

This repository includes nf-ast-grep MCP tools for Nextflow-specific searches:

• nf-ast-grep_find_processes - Find all process definitions
• nf-ast-grep_find_workflows - Find workflow definitions
• nf-ast-grep_find_channels - Find channel factory operations
• nf-ast-grep_find_deprecated - Find deprecated patterns
• nf-ast-grep_lint - Run lint rules on Nextflow code
• nf-ast-grep_search - Search with custom patterns

Use these tools for Nextflow work instead of raw ast-grep commands when available.

Shell Execution

When running ast-grep from bash:

• Single quotes preserve $ metavariables: ast-grep run --pattern 'console.$METHOD'
• Escape in double quotes: ast-grep run --pattern "console.\$METHOD"
• For complex patterns, use --inline-rules with a heredoc or rule files

When to Delegate

• Large searches: Use explore agents for searching across large codebases
• Simple patterns: Run ast-grep directly for quick one-off searches
• Rule development: Use iterative bash commands with --debug-query

Error Handling

"Pattern not matching expected code"

Cause: Pattern syntax doesn't match AST structure.

Solution:

1. Inspect actual AST: ast-grep run --pattern '$$$' --debug-query=ast file.ext
2. Check node kinds match what you expect
3. Simplify pattern and add constraints incrementally

"ast-grep: command not found"

Cause: ast-grep not installed or not in PATH.

Solution:

Copy# Install via cargo
cargo install ast-grep

# Or via npm
npm install -g @ast-grep/cli

# Or via nix
nix shell nixpkgs#ast-grep

"Language not supported"

Cause: Trying to use an unsupported or unconfigured language.

Solution:

• Check supported languages: ast-grep --help
• For custom languages (like Nextflow), ensure sgconfig.yml is present with customLanguages configured
• See Nextflow Reference for custom language setup

"Missing stopBy in relational rule"

Cause: Relational rules (inside, has, precedes, follows) default to stopBy: neighbor which only checks immediate children.

Solution: Always add stopBy: end to search the full subtree:

Copyrule:
  has:
    pattern: target_pattern
    stopBy: end  # Don't forget this!

"Metavariable not captured"

Cause: Using _ prefix makes metavariables non-capturing, or metavariable used before it's defined.

Solution:

• Use $VAR (or _VAR in Nextflow) for capturing
• In all blocks, define metavariables before using them (rules process in order)

Shell escaping issues

Cause: $ in patterns gets interpreted as shell variable.

Solution:

Copy# Use single quotes (preferred)
ast-grep run --pattern 'console.$METHOD'

# Or escape in double quotes
ast-grep run --pattern "console.\$METHOD"

# Or use rule files to avoid shell entirely
ast-grep scan --rule my-rule.yaml

"Rule file not found" or YAML errors

Cause: Invalid YAML syntax or wrong file path.

Solution:

1. Validate YAML syntax (check indentation, colons, quotes)
2. Use absolute paths or run from correct directory
3. Test with --inline-rules first before creating rule file

Examples

Example 1: Finding and Fixing Deprecated Nextflow Patterns

User request: "Find all uses of the deprecated Channel.from() in our Nextflow pipeline"

Workflow:

Copy# Step 1: Quick search to see scope of problem
ast-grep run --pattern 'Channel.from(___)' --lang nextflow

# Step 2: If many results, use the lint tool for structured output
# (uses existing deprecated-channel-from.yaml rule)

Rule used (deprecated-channel-from.yaml):

Copyid: deprecated-channel-from
language: nextflow
severity: warning
message: "Channel.from() is deprecated in DSL2"
note: |
  Use Channel.of() for simple values or Channel.fromList() for lists.
  
  Before: Channel.from(1, 2, 3)
  After:  Channel.of(1, 2, 3)
rule:
  pattern: Channel.from(___)

Result: Found 3 instances in main.nf, updated to use Channel.of().

---

Example 2: Refactoring Console Logging Across a Codebase

User request: "Replace all console.log calls with our custom logger"

Workflow:

Copy# Step 1: Find all console.log calls
ast-grep run --pattern 'console.log($$$ARGS)' --lang js

# Step 2: Create a rewrite rule
cat > /tmp/replace-console.yaml << 'EOF'
id: replace-console-log
language: javascript
rule:
  pattern: console.log($$$ARGS)
fix: logger.info($$$ARGS)
EOF

# Step 3: Preview changes
ast-grep scan --rule /tmp/replace-console.yaml

# Step 4: Apply changes (with --update-all)
ast-grep scan --rule /tmp/replace-console.yaml --update-all

Key insight: The fix field in rules enables automatic refactoring, not just finding.

---

Example 3: Creating a Custom Linting Rule from Scratch

User request: "Create a rule that warns when async functions don't have error handling"

Workflow:

Copy# Step 1: Create example code to understand the AST
cat > /tmp/example.js << 'EOF'
async function good() {
  try {
    await fetch('/api');
  } catch (e) {
    console.error(e);
  }
}

async function bad() {
  await fetch('/api');  // No try-catch!
}
EOF

# Step 2: Inspect AST structure
ast-grep run --pattern '$$$' --debug-query=ast /tmp/example.js

# Step 3: Write initial pattern for async functions with await
ast-grep run --pattern 'async function $NAME($$$) { $$$ }' /tmp/example.js

# Step 4: Add constraint: must have await but no try statement
cat > /tmp/async-error-handling.yaml << 'EOF'
id: async-needs-error-handling
language: javascript
severity: warning
message: "Async function '$NAME' has await but no try-catch"
note: |
  Async functions with await should have error handling.
  Wrap await calls in try-catch blocks.
rule:
  all:
    - pattern: async function $NAME($$$PARAMS) { $$$BODY }
    - has:
        pattern: await $$$
        stopBy: end
    - not:
        has:
          kind: try_statement
          stopBy: end
EOF

# Step 5: Test the rule
ast-grep scan --rule /tmp/async-error-handling.yaml /tmp/example.js

Result: Rule correctly flags bad() but not good().

---

Example 4: Finding Implicit Closure Parameters in Nextflow

User request: "Find closures that use implicit 'it' parameter - we want explicit parameters for readability"

Workflow:

Copy# Use the existing rule via nf-ast-grep tools
# Or run directly:
ast-grep scan --rule config/opencode/skills/ast-grep/rules/implicit-it-closure.yaml

Rule explanation (implicit-it-closure.yaml):

Copyid: implicit-it-closure
language: nextflow
severity: hint
message: "Consider using explicit closure parameter instead of implicit 'it'"
rule:
  all:
    - kind: closure
    - has:
        pattern: it
        stopBy: end
    - not:
        has:
          kind: closure_parameter
          stopBy: end

This uses kind matching (AST node type) combined with has/not has to find closures that reference it but don't declare a parameter.

---

Example 5: Multi-Pattern Search with Dependencies

User request: "Find all React components that use useState but don't have a useEffect cleanup"

Workflow:

Copycat > /tmp/missing-cleanup.yaml << 'EOF'
id: missing-useeffect-cleanup
language: typescript
severity: warning
message: "Component uses useState but may be missing useEffect cleanup"
rule:
  all:
    - kind: function_declaration
    - has:
        pattern: useState($$$)
        stopBy: end
    - has:
        pattern: useEffect($$$)
        stopBy: end
    - not:
        has:
          pattern: |
            useEffect(() => {
              $$$SETUP
              return $$$CLEANUP
            }, $$$DEPS)
          stopBy: end
EOF

ast-grep scan --rule /tmp/missing-cleanup.yaml src/

Key insight: Complex patterns can combine multiple has and not has clauses to express sophisticated constraints.

References

For detailed syntax and advanced features, see:

• Rule Reference - Complete rule syntax documentation
• Nextflow Reference - Nextflow-specific patterns and examples

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Progressive Disclosure

This skill document provides a practical introduction to ast-grep. For deeper understanding:

1. Start here - Quick reference and common patterns cover 80% of use cases
2. Rule Reference - When you need advanced rule syntax (relational rules, transformations)
3. Nextflow Reference - For Nextflow-specific work (custom language config, real examples)
4. ast-grep docs - For edge cases: https://ast-grep.github.io/