Parse and inspect Nextflow DSL scripts to extract information from Nextflow workflows, processes, channels, and more.
- 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.
pip install nf-parser- python >=3.9
- lark
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}")
Detailed documentation, including available methods and data structures, can be found in the documentation.
pytest
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