Linting a workflow

The lint subcommand checks a given pipeline for all nf-core community guidelines. This is the same test that is used on the automated continuous integration tests.

For example, the current version looks something like this:

You can use the -k / --key flag to run only named tests for faster debugging, eg: nf-core pipelines lint -k files_exist -k files_unchanged. The nf-core pipelines lint command lints the current working directory by default, to specify another directory you can use --dir <directory>.

Linting documentation

Each test result name on the left is a terminal hyperlink. In most terminals you can ctrl + click ( cmd + click) these links to open documentation specific to this test in your browser.

Alternatively visit https://nf-co.re/tools/docs/latest/pipeline_lint_tests/ and find your test to read more.

Linting config

It’s sometimes desirable to disable certain lint tests, especially if you’re using nf-core/tools with your own pipeline that is outside of nf-core.

To help with this, you can add a tools config file to your pipeline called .nf-core.yml in the pipeline root directory (previously: .nf-core-lint.yml). Here you can list the names of any tests that you would like to disable and set them to False, for example:

lint:
  actions_awsfulltest: False
  pipeline_todos: False

Some lint tests allow greater granularity, for example skipping a test only for a specific file. This is documented in the test-specific docs but generally involves passing a list, for example:

lint:
  files_exist:
    - CODE_OF_CONDUCT.md
  files_unchanged:
    - assets/email_template.html
    - CODE_OF_CONDUCT.md

Note that you have to list all configurations for the nf-core pipelines lint command under the lint: field in the .nf-core.yml file, as this file is also used for configuration of other commands.

Automatically fix errors

Some lint tests can try to automatically fix any issues they find. To enable this functionality, use the --fix flag. The pipeline must be a git repository with no uncommitted changes for this to work. This is so that any automated changes can then be reviewed and undone (git checkout .) if you disagree.

Lint results output

The output from nf-core pipelines lint is designed to be viewed on the command line and is deliberately succinct. You can view all passed tests with --show-passed or generate JSON / markdown results with the --json and --markdown flags.