Null Items Dropped From Lists When Returning From Process Tests

[emarinier]

When I try to test that a null value can be returned within a list from a process, it appears that nf-test is dropping the null values from the list. I've created the following example to demonstrate the problem:

main.nf

include { return_null } from './return_null.nf'

workflow {
    return_null | view { it }
}

return_null.nf

process return_null {

    output:
    val null_list, emit: null_list

    exec:
    null_list = ["0", "1", "", null, "4"]
}

return_null.nf.test

nextflow_process {

    name "Test Process return_null"
    script "return_null.nf"
    process "return_null"

    test("Should run without failures") {

        when {
            params {}
            process {}
        }

        then {
            assert process.success

            with(process.out) {
                assert null_list == [["0", "1", "", null, "4"]]
            }
        }

    }

}

Nextflow seems to support this behaviour:

$ nextflow run main.nf 
N E X T F L O W  ~  version 23.04.3
Launching `main.nf` [agitated_kimura] DSL2 - revision: 7bdd792613
executor >  local (1)
[dd/20ca57] process > return_null [100%] 1 of 1 ✔
[0, 1, , null, 4]

However, nf-test does not seem to support it:

$ nf-test test

🚀 nf-test 0.8.2
https://code.askimed.com/nf-test
(c) 2021 - 2023 Lukas Forer and Sebastian Schoenherr

Found 1 files in test directory.

Test Process return_null

  Test [36f973af] 'Should run without failures' FAILED (3.857s)

  Assertion failed: 
  
  assert null_list == [["0", "1", "", null, "4"]]
         |         |
         |         false
         [['0', '1', '', '4']]
  
  Nextflow stdout:
  
  Nextflow stderr:
  
  



FAILURE: Executed 1 tests in 3.862s (1 failed)

I'm not familiar with the nf-test project, but I dug around a bit, and my best guess is that during JSON serialization of the channel (here), a JsonGenerator object is used with the .excludeNulls() option set (here). The corresponding outputs in meta/output_0.json and meta/output_null_list.json have the null item missing, so it seems to be related to serialization:

{"null_list":[["0","1","","4"]]}

Anyways, I'm not sure what the expected behaviour for nf-test is supposed to be, but I thought I would mention it here, since it seems to be different than Nextflow.

[lukfor]

Thanks!

This is fixed in PR #232