How to handle module specific parameters

[tischi]

Some modules accept module specific parameters, e.g. --diameter for CellPose.

Maybe I am overlooking it, but currently for the cellpose module in our repo I could not find a documentation for how to specify such parameters.

I had a look at the nf-core molkart pipeline and they handle this in two places, namely nextflow.config and modules.config:

• https://github.com/nf-core/molkart/blob/master/nextflow.config#L19
• https://github.com/nf-core/molkart/blob/master/conf/modules.config#L205

In this documentation they seem to suggest to have a configs/cellpose.config file that could be included in the nextflow.config via includeConfig 'configs/cellpose.config'.

I am wondering now whether our modules repositories could somewhere contain for each module such a module specific .config file that one could copy when installing/using this module a pipeline? In my mind that would make it much easier to know which additional module specific parameters one can use.

ping @krokicki @BioinfoTongLI

[BioinfoTongLI]

I believe, in general, regardless the algorithm, the optional (the ones not explicitly listed in the input section) parameters should go with ext.args = xxxx. And that should apply to all modules.

I am personally putting examples directly in the main.nf.test.
https://github.com/cellgeni/nf-modules/blob/main/modules/sanger-cellgeni/imaging/tiledspotiflow/tests/main.nf.test#L18-L22
but in term of general options, I don't have it now. The easiest way for me would be starting the container the run the CLI with --help flag.

[tischi]

And how do you feel about adding a configs folder to our modules repositories, with one .config file for each module?

[BioinfoTongLI]

I think it wont' hurt. But what exactly do you want to put inside it?

[tischi]

That's what they did in molkart. It seems that they are prepending <module>_ to the parameters and convert those to actual module parameters in the config; I guess this is to avoid potential clashes with parameters of other modules?

[BioinfoTongLI]

I'd say you can do that. Only when you have to pass it through nextflow. Otherwise, you can directly do:

process {
    withName: CELLPOSE {
        ext.args = <all my cellpose params>
    }
    withName: MYOTHERMODULE {
        ext.args = <all my other params>
    }
}

and they won't clash. AFAIK.
Also, I don't think they are exposing all possible parameters there. so, there will still be missing params from that config. Thus, it doesn't replace the proper read-the-doc webpage.
My personal opinion will be: yes, we can put something there as the default value if they are missing.
But if that's all it meant to serve. Why not write the default value in your executable script directly? python/java etc.