Hi, I would like to clarify something regarding nf-schema defaults. I am allowing parameters via samplesheet, or params. The idea is that samplesheet should take priority, but if the param is not set per-sample there should be a fallback to the param. Here is what I am doing

channel.fromList(samplesheetToList(params.input, "assets/schema_input.json"))
        /*
        This is a somewhat crucial step, where the samplesheet and params are used to determine per-sample parameters.
        This has been greatly simplified thanks to @nvnieuwk
        */
        .map { it ->
            def meta = it[0]
            // Populate everything that has no value with the value from params
            return meta.collectEntries { key, val -> key == "group" ? [ key, val ] : [ key, val ?: params.get(key) ] }
        }

1. However, I also set

defaults

in

schema_inputs

. As I understand, this probably breaks what I want to do, and I should rather remove the defaults from the schema, to ensure that this actually falls back to params? To do this: should I remove defaults? Will I still receive an entry if there is no default and it was not in the samplesheet? Should I set defaults to

null

? 2. Something about this that has been bothering me for a while is: I assume that if a user were to set a

param.something = true

and in the samplesheet would provide

something

as

false

, this would actually override the per-sample value false with the param value true, because

val ?: params.get(key)

would get it from params, since the condition is false. Is there some established pattern to handle this?

This system only works for values specified in the samplesheet. It doesn't work for schema defaults (although it is something that I could implement if needed, feel free to open an issue if you want this.) I'd suggest removing the defaults from the schema if you specify the defaults in your pipeline code. This will automatically set all values to

[]

if they are missing, you could also set the default to

null

if you'd prefer that for your logic

Thanks a lot. I will remove the defaults. Just to clarify: even if there is no default, the respective k/v pair will come out of

samplesheetToList(params.input, "assets/schema_input.json")

with a value of

[]

, if it is listed in the schema, but not part of the actual samplesheet?

Yes! The structure of each samplesheet entry will be the same 🙂