nf_core.lint

Linting policy for nf-core pipeline projects.

Tests Nextflow-based pipelines to check that they adhere to the nf-core community guidelines.

nf_core.lint.run_linting(pipeline_dir, release_mode=False, fix=(), key=(), show_passed=False, fail_ignored=False, fail_warned=False, sort_by='test', md_fn=None, json_fn=None, hide_progress=False)

Runs all nf-core linting checks on a given Nextflow pipeline project in either release mode or normal mode (default). Returns an object of type PipelineLint after finished.

• Parameters:
  • pipeline_dir (str) – The path to the Nextflow pipeline root directory
  • release_mode (bool) – Set this to True, if the linting should be run in the release mode. See PipelineLint for more information.
• Returns: An object of type PipelineLint that contains all the linting results.

classnf_core.lint.PipelineLint(wf_path, release_mode=False, fix=(), key=None, fail_ignored=False, fail_warned=False, hide_progress=False)

Bases: Pipeline

Object to hold linting information and results.

Inherits nf_core.utils.Pipeline class.

Use the PipelineLint._lint_pipeline() function to run lint tests.

• Parameters: path (str) – The path to the nf-core pipeline directory.

failed

A list of tuples of the form: (<test-name>, <reason>)

• Type: list

ignored

A list of tuples of the form: (<test-name>, <reason>)

• Type: list

lint_config

The parsed nf-core linting config for this pipeline

• Type: dict

passed

A list of tuples of the form: (<test-name>, <reason>)

• Type: list

release_mode

True, if you the to linting was run in release mode, False else.

• Type: bool

warned

A list of tuples of the form: (<warned no>, <reason>)

• Type: list

_get_results_md()

Create a markdown file suitable for posting in a GitHub comment.

• Returns: Formatting markdown content
• Return type: markdown (str)

_lint_pipeline()

Main linting function.

Takes the pipeline directory as the primary input and iterates through the different linting checks in order. Collects any warnings or errors into object attributes: passed, ignored, warned and failed.

_print_results(show_passed)

Print linting results to the command line.

Uses the rich library to print a set of formatted tables to the command line summarising the linting results.

_save_json_results(json_fn)

Function to dump lint results to a JSON file for downstream use

• Parameters: json_fn (str) – File path to write JSON to.

_wrap_quotes(files)

Helper function to take a list of filenames and format with markdown.

• Parameters: files (list) –

  List of filenames, eg:

  ['foo', 'bar', 'baz']

• Returns: Formatted string of paths separated by word or, eg:

  `foo` or bar` or `baz`

• Return type: markdown (str)