I found that the nf-test test arg

--profile=<profile>   Profile to execute all tests

wipes the test profile, leading to errors caused by wiping of any params set in the test profile (e.g.

input

). For example, if I run in a pipeline repo:

nf-test test --profile singularity

I get errors such as:

The following invalid input values have been detected:

  * Missing required parameter(s): input

because these params are set in the test profile:

params {
    config_profile_name        = 'Test profile'
    config_profile_description = 'Minimal test dataset to check pipeline function'

    // Input data
    input  = params.pipelines_testdata_base_path + 'hlatyping/samplesheets/samplesheet_bam.csv'
}

However, if I run:

nf-test test --profile test,singularity tests/default.nf.test

the test passes, but I have to manually match up each test profile to the test file. Is there a better canonical way to do this?

Not sure if I fully understand your issue, but you can specify which test profile to use in

nf-test.config

via

config { profile "test" }

to specify the test profile to be tested with

nf-test test

--profile=+singularity

as Matthias said

Neat, didn't know you could append like that!