nf_test_content

PipelineLint.nf_test_content() → Dict[str, List[str]]

Checks that the pipeline nf-test files have the appropriate content.

This lint test checks the following files and content of these files:

• *.nf.test files should specify the outdir parameter:

when {
    params {
        outdir = "$outputDir"
    }
}

• A versions.yml file should be included in the snapshot of all *.nf.test files

• The nextflow.config file should contain:

  modules_testdata_base_path = <path>

  and

  pipelines_testdata_base_path = <path>

  And should set the correct resource limits, as defined in the test profile

• The nf-test.config file should:

  • Make sure tests are relative to root directory
    

  testsDir "."

  
  * Ensure a user-configurable nf-test directory

  workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"

  
  * Use a test specific config
  ```groovy configFile "tests/nextflow.config" ```

All these checks can be skipped in the .nf-core.yml file using:

lint:
  nf_test_content: False

or

lint:
  nf_test_content:
    - tests/<test_name>.nf.test
    - tests/nextflow.config
    - nf-test.config