reftrace 0.0.0

Lint Nextflow pipelines in Python

RefTrace

Lint Nextflow pipelines in Python.

pip install reftrace

Features

• Write custom linting rules in Python.
• Avoid parsing the Nextflow DSL.
• Access the Nextflow DSL from Python.

Example Rule

@rule
def no_labels(module: Module, results: LintResults):
    for process in module.processes:
        if not process.labels:
            results.warnings.append(
                ModuleWarning(
                    line=process.line,
                    warning=f"process '{process.name}' has no labels"
                )
            )

Getting Started

Run in your pipeline directory:

reftrace generate  # Create rules.py starter rules
reftrace lint

You'll get output like this:

Module: /home/andrew/nf-core/rnaseq/modules/nf-core/preseq/lcextrap/main.nf
  Warning on line 1: process 'PRESEQ_LCEXTRAP' has non-standard labels: ['error_ignore']

Module: /home/andrew/nf-core/rnaseq/modules/nf-core/hisat2/build/main.nf
  Warning on line 1: process 'HISAT2_BUILD' has conflicting labels: ['process_high', 'process_high_memory']

RefTrace automatically runs the linting rules in rules.py on all modules in the pipeline.

Access Nextflow from Python

from reftrace import Module

module = Module("path/to/nextflow.nf")

Limitations

• Not all parts of the Nextflow DSL are yet exposed. Specifically, only processes are handled. Only directives, process inputs, and process outputs are exposed to linting rules.

• The parser is not perfect. It doesn't seek to handle all of Groovy, but enough to work in practice. Even so, test coverage could be better. If you encounter a parsing bug, please open an issue.

Acknowledgements

We would like to express our gratitude to the following:

• The Apache Groovy project.
• The ANTLR project, for providing the parser generator used in this tool.
• The Go programming language and its standard library.
• The Nextflow project and community, for being so welcoming and helpful.

License

This project is licensed under the Apache License, Version 2.0. See the LICENSE file for details.