Hello! About

params.pipelines_testdata_base_path

, why is it necessary to include it in duplicate, both in

nextflow.config

and

tests/nextflow.config

? 🤔 I searched for information here in Slack and in previous PRs but couldn't quite get the reasoning behind this choice. I was looking into how we could avoid duplicating the parameter definition to make it easier to update in the future, but ran into these problems: • If removed from

tests/nextflow.config

, nf-test works but a linting error is thrown. (Additionally, if parameters are added here that depend on params from the main config, the tests cannot run.) • If removed from

nextflow.config

, when using the test profile, parameters in the

conf/test.config

that use this path cannot be resolved.

Yeah, I'm afraid both are still needed for now

For what reason though? Does it have to do with the order/how the configs are loaded? I am a bit confused about that. 😵‍💫

My assumption, nf-test resolves the config files after the params in the scope

It should be enough to just have it in

nextflow.config

as nf-test just adds the

tests/nextflow.config

configuration using

-c

. What is exactly throwing the linting error? Is it the nf-core tooling?

Yeah, that's what I thought too. But this is the linting error:

nf_test_content: 'tests/nextflow.config' does not contain pipelines_testdata_base_path

Looks like this was proposed in this issue https://github.com/nf-core/tools/issues/3064 but the reason for it is not stated.

Yeah that could be safely removed from tools, the check should be expanded to check if it's in

nextflow.config

instead.

Alright! Thank you both for your replies! 🌟 I went ahead and opened an issue to document this: https://github.com/nf-core/tools/issues/4176

Thank you!