Hi! I wanted to know if it's possible to show nested parameters on the parameters section of the docs? I have a pipeline (in dev mode) with nested parameters, but only the parent group is shown here, although the nextflow_schema is properly documenting all the parameters Any idea? 🙂

No, we've never allowed nested parameters (even if we didn't lint/check for it, TBF), because apparently it is a horrible can of worms

It seems to work really well for me at least Using a

-params-file

make it very convenient to provide nested arguments

Ah sorry to be clear I mean it doesn't work well with rendering on website/launch stuff

It was a decision we made when designing the schema. There is an issue open about adding support for it, but we put it on ice as longer term support in Nextflow is unlikely

In my case, having nested params is necessary: we support multiple segmentation tools, and they all come with their own config. For instance,

params.segmentation.baysor

for parameters specific to baysor (a segmentation tool) - see example here, or

params.segmentation.proseg

. If we flatten the params, we loose the original official baysor parameter names, and we’ll need to do a manual mapping for every single one. The second reason is that, by default, we don’t know which segmentation tool(s) will be used. Therefore, having groups is a good way to check which tool to run: e.g. if there is something in the

baysor

params, we run baysor. If we flatten everything, we’ll need global defaults, but they need to be provided per group (we either all or none params of each group).

Feel free to hop on the thread above and make your case (better placed than here)