A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

could i get some insights from other maintainers on how they are using parameter sets dependent on which technology was used for the data generation: <https://github.com/nf-core/sopa/pull/11#issuecomment-3402504359>

Do you mean?
```process {
    withName: 'SOMETOOL' {
        ext.args = { [
            "--opt1",
            params.method == "method1" ? "--optX" : "",
            params.method in ["method2", "method3"] ? "--optY" : "--optZ",
        ].minus("").join(" ") }
    }
}```

What do you mean by pipeline level? Do you mean config profiles that set a bunch of parameters?

i was also thinking of using different configs, but wasn't sure if there was a better solution out there

Using profiles would probably be the preferred way if there's a small set of options to choose from.

One could probably use `includeConfig` to include the correct config depending on the pipeline parameter too.

it is quite an long list of parameters it looks like: e.g. <https://github.com/gustaveroussy/sopa/blob/main/workflow/config/xenium/baysor.yaml>

Yeah, I would go with that. Use `includeConfig` to include the desired config settings including extra parameters

feel free to post this on the PR, so you get accredited :wink: