nf_core.lint

Tip

See the Lint Tests docs for information about specific linting functions.

Linting policy for nf-core pipeline projects.

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

nf_core.pipelines.lint.run_linting(pipeline_dir, release_mode: bool = False, fix=(), key=(), show_passed: bool = False, fail_ignored: bool = False, fail_warned: bool = False, sort_by: str = 'test', md_fn=None, json_fn=None, hide_progress: bool = False) → Tuple[PipelineLint, ComponentLint | None, ComponentLint | None]

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. An object of type ComponentLint that contains all the linting results for the modules. An object of type ComponentLint that contains all the linting results for the subworkflows.