Process Testing

nf-test allows to test each process defined in a module file. Please checkout the CLI to generate a process test.

Syntax

nextflow_process {

    name "<NAME>"
    script "<PATH/TO/NEXTFLOW_SCRIPT.nf>"
    process "<PROCESS_NAME>"

    test("<TEST_NAME>") {

    }
}

Script paths that start with ./ or ../ are considered relative paths. These paths are resolved based on the location of the test script. Relative paths are beneficial when you want to reference files or directories located within the same directory as your test script or in a parent directory. These paths provide a convenient way to access files without specifying the entire path.

Assertions

The process object can be used in asserts to check its status or error messages.

// process status
assert process.success
assert process.failed
assert process.exitStatus == 0

// Analyze Nextflow trace file
assert process.trace.tasks().size() == 1

// process error message
assert process.errorReport.contains("....")

//returns a list containing all lines from stdout
assert process.stdout.contains("Hello World") == 3

Output Channels

The process.out object provides access to the content of all named output Channels (see Nextflow emit):

// channel exists
assert process.out.my_channel != null

// channel contains 3 elements
assert process.out.my_channel.size() == 3

// first element is "hello"
assert process.out.my_channel.get(0) == "hello"

Channels that lack explicit names can be addressed using square brackets and the corresponding index. This indexing method provides a straightforward way to interact with channels without the need for predefined names. To access the first output channel, you can use the index [0] as demonstrated below:

// channel exists
assert process.out[0] != null

// channel contains 3 elements
assert process.out[0].size() == 3

// first element is "hello"
assert process.out[0].get(0) == "hello"

Example

Nextflow script

Create a new file and name it say_hello.nf.

#!/usr/bin/env nextflow
nextflow.enable.dsl=2

process SAY_HELLO {
    input:
        val cheers

    output:
        stdout emit: verbiage_ch
        path '*.txt', emit: verbiage_ch2

    script:
    """
    echo -n $cheers
    echo -n $cheers > ${cheers}.txt
    """
}

nf-test script

Create a new file and name it say_hello.nf.test.

nextflow_process {

    name "Test Process SAY_HELLO"
    script "say_hello.nf"
    process "SAY_HELLO"

    test("Should run without failures") {

        when {
            process {
                """
                input[0] = Channel.from('hello','nf-test')
                """
            }
        }

        then {

            assert process.success
            assert process.trace.tasks().size() == 2

            with(process.out.verbiage_ch2) {
                assert size() == 2
                assert path(get(0)).readLines().size() == 1
                assert path(get(1)).readLines().size() == 1
                assert path(get(1)).md5 == "4a17df7a54b41a84df492da3f1bab1e3"
            }

        }

    }
}

Execute test

nf-test init
nf-test test say_hello.nf.test