tree-sitter-nextflow

Nextflow grammar for tree-sitter.

Target: Nextflow Strict Syntax (v2 Parser) - NXF_SYNTAX_PARSER=v2

This grammar is designed to support Nextflow's strict syntax mode, focusing on the cleaner, more consistent v2 parser syntax patterns.

Features

• Core Nextflow Syntax: Process definitions, workflows, variable declarations
• Language Injection: Bash/shell syntax highlighting in script blocks
• Expressions: Binary operators, lists, maps, function calls
• Control Flow: If/else statements, blocks
• Channel Operations: Channel.from(), Channel.value(), Channel.of() with pipe operations

Development Status

Current Test Coverage: 28/80 tests passing (35%)

• ✅ Core Features: Variable declarations, process definitions, script injection
• ✅ Expressions: Binary operations, lists, maps, channel operations
• ✅ Control Flow: If/else statements, function calls
• 🚧 In Progress: String interpolation, advanced workflows, closures
• ⏳ Future: Configuration files, error handling, advanced channel operators

AST-grep Integration

This grammar includes full ast-grep support for advanced Nextflow code analysis, linting, and refactoring.

Quick Install

Install ast-grep support with a single command:

curl -fsSL https://raw.githubusercontent.com/nextflow-io/tree-sitter-nextflow/main/scripts/install-ast-grep.sh | bash

For global installation:

curl -fsSL https://raw.githubusercontent.com/nextflow-io/tree-sitter-nextflow/main/scripts/install-ast-grep.sh | bash -s -- --global

Installation

Option 1: Automated Installation (Recommended)

Use the installation script to set up ast-grep for your project:

# Clone or download the repository
git clone https://github.com/nextflow-io/tree-sitter-nextflow.git
cd tree-sitter-nextflow

# Run the installation script
./scripts/install-ast-grep.sh

# Or install globally
./scripts/install-ast-grep.sh --global

The script will:

• Detect your platform (macOS, Linux)
• Verify the appropriate parser library exists
• Copy sgconfig.yml to your project or ~/.config/ast-grep/

Option 2: Manual Installation

If you prefer manual setup or need a custom configuration:

# 1. Copy sgconfig.yml to your Nextflow project
cp path/to/tree-sitter-nextflow/sgconfig.yml .

# 2. Update libraryPath if needed (for global install)
# Edit sgconfig.yml and use absolute paths to lib/ directory

Platform Support

Pre-built parser libraries are included for:

• ✅ macOS ARM64 (Apple Silicon) - lib/macos-arm64/libnextflow.dylib
• ✅ Linux x64 - lib/linux-x64/libnextflow.so

For other platforms, you can build the library yourself:

tree-sitter build --output libnextflow.so

Quick Start

Once installed, ast-grep works seamlessly with Nextflow files:

# Search for process definitions
ast-grep -l nextflow -p 'process _NAME { ___ }' .

# Run built-in rules
ast-grep scan

# Find deprecated Channel.from() usage
ast-grep -l nextflow -p 'Channel.from($___)' .

Configuration

The project includes sgconfig.yml with platform-specific parser libraries:

• Custom Language: Nextflow with platform detection
• File Extensions: .nf, .config
• expandoChar: _ (use _VAR instead of $VAR in patterns, since Nextflow uses $ for string interpolation)

Built-in Rules

The rules/ directory includes linting rules for:

• Process naming conventions: Enforce UPPERCASE or camelCase naming
• Channel operations: Detect deprecated patterns (Channel.from, into, separate)
• DSL2 best practices: Workflow structure, tuple inputs, named emits
• String interpolation: Single vs double quotes, GString usage

Pattern Examples

# Find all process definitions
ast-grep -l nextflow -p 'process _NAME { ___ }'

# Find workflows with take/main/emit structure
ast-grep -l nextflow -p 'workflow _NAME { take: ___ main: ___ emit: ___ }'

# Find deprecated Channel.from() (flagged by rules)
ast-grep -l nextflow -p 'Channel.from($$$)'

# Search for hardcoded paths
ast-grep -l nextflow -p 'path("/___")'

# Find string interpolation
ast-grep -l nextflow -p '"$___"'

Note: Use _ instead of $ in patterns due to expandoChar configuration.

Custom Rules

Create YAML files in rules/ directory:

id: my-custom-rule
language: nextflow
message: Custom rule message
severity: warning
rule:
  pattern: process _NAME { ___ }

See ast-grep rule documentation for details.

Benefits

• Code Search: Fast semantic search across Nextflow codebases
• Refactoring: Automated migrations (e.g., DSL1 → DSL2)
• Linting: Enforce coding standards and best practices
• CI/CD: Integrate rules into continuous integration pipelines

References

• Nextflow ANTLR grammar
• Nextflow TextMate grammar
• AST-grep Custom Languages