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scverse / spatialdata-io

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Question about naming tool/subtool for nf-core module #27

Open FloWuenne opened 1 year ago

FloWuenne commented 1 year ago

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 commented 1 year ago

Hi Flo, thanks for your contribution!

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

FloWuenne commented 11 months ago

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 commented 10 months ago

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

melonora commented 10 months ago

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

FloWuenne commented 10 months ago

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 commented 10 months ago

As soon as I have time I want to pick up https://github.com/scverse/spatialdata-io/pull/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 commented 9 months ago

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