Philosophy of nf-tests for nf-core components

  • Each component contains a tests/ folder beside the main.nf of the component itself, containing the test files.
  • Test files come with a snapshot of component output channels.

nf-test guidelines for a simple un-chained module

  • Some modules MAY require additional parameters added to the test command to successfully run. These can be specified using a params input and an ext.args variable within the process scope of the nextflow.config file that exists alongside the test files themselves (and is automatically loaded when the test workflow main.nf is executed).

If your module requires a nextflow.config file to run, create the file to the module’s tests/ directory and add the following code to use parameters defined in the when scope of the test.

touch modules/nf-core/<tool>/<subtool>/tests/nextflow.config
nextflow.config
process {
  withName: 'MODULE' {
    ext.args = params.module_args
  }
}

You do not need to modify the contents of this file any further.

Then add the config to the main.nf.test file.

main.nf.test
process "MODULE"
config "./nextflow.config"

Lastly supply the params in the when section of the test.

main.nf.test
config './nextflow.config'
 
when {
  params {
    module_args = '--extra_opt1 --extra_opt2'
  }
  process {
    """
    input[0] = [
      [ id:'test1', single_end:false ], // meta map
      file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true)
    ]
    """
  }
}

  • When your test data is too big, the tests take too long or require too much resources, you can opt to run your tests in stub mode by adding the following option:

    main.nf.test
    options "-stub"
    Note

    this can be added at the top of main.nf.test to have all tests run in stub mode or this can also be added to a single test

Tip

See the assertions documentation for examples on how to handle different types of test data and scenarios.

nf-test guidelines for a chained module

  • For modules that involve running more than one process to generate required test-data (aka chained modules), nf-test provides a setup method.

  • For example, the module abricate/summary requires the process abricate/run to be run prior and takes its output as input. The setup method is to be declared before the primary when block in the test file as shown below:

main.nf.test
setup {
 
            run("ABRICATE_RUN") {
                script "../../run/main.nf"
                process {
                    """
                    input[0] =  Channel.fromList([
                        tuple([ id:'test1', single_end:false ], // meta map
                            file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true)),
                        tuple([ id:'test2', single_end:false ],
                            file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true))
                    ])
                    """
                }
            }
        }
Note

The setup method can run more than one process each enclosed in their own run block

  • Then, the output of setup process/es can be provided as input in the process section of when block
main.nf.test
input[0] = ABRICATE_RUN.out.report.collect{ meta, report -> report }.map{ report -> [[ id: 'test_summary'], report]}
  • Next, in the then block we can write our assertions that are used to verify the test. A test can have multiple assertions but, we recommend enclosing all assertions in a assertAll() block as shown below:
main.nf.test
assertAll(
            { assert process.success },
            { assert snapshot(process.out).match() }
          )
  • the main.nf.test file for chained modules will finally look as shown below:
main.nf.test
nextflow_process {
 
    name "Test Process ABRICATE_SUMMARY"
    script "../main.nf"
    process "ABRICATE_SUMMARY"
    tag "modules"
    tag "modules_nfcore"
    tag "abricate"
    tag "abricate/summary"
 
    test("bacteroides_fragilis - genome_fna_gz") {
 
        setup {
            run("ABRICATE_RUN") {
                script "../../run/main.nf"
                process {
                """
                input[0] = Channel.fromList([
                                tuple([ id:'test1', single_end:false ], // meta map
                                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true)),
                                tuple([ id:'test2', single_end:false ],
                                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true))
                            ])
                """
            }
            }
        }
 
        when {
            process {
                """
                input[0] = ABRICATE_RUN.out.report.collect{ meta, report -> report }.map{ report -> [[ id: 'test_summary'], report]}
                """
            }
        }
 
        then {
            assertAll(
                { assert process.success },
                { assert snapshot(process.out).match() }
            )
        }
    }
}
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