nf-parser

Parse and inspect Nextflow DSL scripts to extract information from Nextflow workflows, processes, channels, and more.

Features

• DSL Parsing: Parse Nextflow DSL scripts to extract structured information.
• Workflow Analysis: Retrieve details about workflows, processes, channels, and other components.
• Channel Operators: Parse and understand Nextflow channel operators for further analysis.
• DAG Generation: Generate a Directed Acyclic Graph (DAG) of the workflow for visualization and analysis.
• Syntax Validation: Validate Nextflow syntax to catch errors early in the development process.

Installation

pip install nf-parser

Dependecies

• python >=3.9
• lark

Usage

from nf_parser import NextflowParser

# Example usage
script = """
workflow example {
    input:
    path data

    script:
    """
    cat ${data} > output.txt
    """
}
"""

# Parse the script
parser = NextflowParser()
parsed_data = parser.parse(script)

# Access parsed information
workflow_name = parsed_data["workflows"][0]["name"]
print(f"Workflow Name: {workflow_name}")

# Generate a DAG
dag = NextflowDAG(parsed_data)
dag.generate_dag()
dag.visualize_dag("workflow_dag.png")

# Validate syntax
is_valid_syntax = parser.validate_syntax(script)
print(f"Is Syntax Valid: {is_valid_syntax}")

Documentation

Detailed documentation, including available methods and data structures, can be found in the documentation.

Testing

pytest

Contributing

Interested in contributing? Check out the contributing guidelines. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.

Credits