Expected behaviour for booleans with no set default

[awgymer]

What is the intended behaviour for a boolean field that does not have a default in the schema but is empty/unset in the samplesheet?

I believe this may be an issue because I was under the impression that we do not support default: false in schema jsons (although maybe I am wrong here?).

Currently if there is no default and someone leaves the field unset it will result in:

in meta:
[boolean_field: null]

otherwise:
[[]]

[nvnieuwk]

This is a really difficult issue to tackle due to the complexity of the new JSON schema. An input can sometimes be more than one type so it's hard to define what the default should be. I'll take a look at this later and see if there maybe is some kind of a compromise to be made

[nvnieuwk]

The easiest solution in this case would be to just set the default to false that way you specifically annotate what value should be the default instead of having an inferred default. Feel free to reopen if you disagree with this :)

[awgymer]

I am not sure what the current status of "default": false is in the schema but nf-core/tools still seems to advise against it:
https://github.com/nf-core/tools/blob/ddb58c20e757e3b2a384a5ccb8ddd2a5b4af59f9/nf_core/pipelines/schema.py#L334C1-L338C18

Perhaps @mirpedrol can shed a bit more light?

[nvnieuwk]

I personally don't like having inferred defaults especially for samplesheets. It just makes everything way more complicated overall IMO.

AFAIK nf-core/tools only has this for the parameters (in which case it is fine because nf-schema doesn't fill in parameter defaults). The tooling does nothing with the samplesheet schema I think

[mirpedrol]

Hi! Yes, the decision of removing default: false is only for parameters, this was done to avoid printing all the parameters when we print the summary of parameters that change (here some Slack conversations about this back when we made the change). We don't have tooling for the schema yet, so you can add a default there :)