Question about naming tool/subtool for nf-core module

[FloWuenne]

Hi everyone,

as discussed, we want to write the MCMICRO spatialdata-io reader (https://github.com/scverse/spatialdata-io/blob/main/src/spatialdata_io/readers/mcmicro.py) as an nf-core DSL2 nextflow module that can collect output from MCMICRO at the end of the pipeline and create a SpatialData object from these files.

We are wondering, how we should name this TOOL/SUBTOOL in the nf-core repo. The nf-core modules repo has tools organized by TOOL/SUBTOOL. For example, samtools/bamt2fq , samtools/markdup etc.

The idea of modules are that they are processes that can't be broken down any further. If we make a module that can collect output from MCMICRO (or any other imaging pipeline) and put them into a SpatialData object, what would we call this?
👍🏻
Also tagging @melonora because he will be joining the hackathon with us!

[LucaMarconato]

Hi Flo, thanks for your contribution!

I'll think about it. Tagging also @kevinyamauchi @ivirshup

[FloWuenne]

Hi @LucaMarconato,

coming back to this, I think for the moment we could go with spatialdata/mcmicro for a module that will collect mcmicro outputs and create a spatialdata structure.

Pinging @melonora, because he has been working on this during some hackathons!

[LucaMarconato]

Sounds good to me! Looking forward to trying it out!

[melonora]

@LucaMarconato @FloWuenne I still have that code somewhere with this naming.

[FloWuenne]

Just to also come back to this question, since we want to add the spatialdata wrapper to nf-core/mcmicro and nf-core/molkart in the near future.

I guess the question really is, whether we will make 1 module that has a CLI to call the different wrapper (and call it spatialdata/spatialdata-io) or we make 1 distinct module for each wrapper (like spatialdata/mcmicro , spatialdata/molkart).

What is your opinion as a developer? Should we put everything in one module that's controlled by 1 CLI, is that feasible enough? Is there an advantage of putting everything in 1 nf-core process/module versus making different ones?

[LucaMarconato]

As soon as I have time I want to pick up #72 and make all the readers of spatialdata-io invokable via CLI. If this is enough for you then I would have just one module spatialdata/spatialdata-io.

[FloWuenne]

That sounds great @LucaMarconato ! Let us know once this is at a useable stage so we can adapt this into nf-core! 😄