reftrace 0.6.0

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.

Test Data

The files in the testdata/groovy_core directory are derived from the Apache Groovy project's test suite and are licensed under the Apache License 2.0. The original source files can be found in the Apache Groovy repository.

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.