new module: scscplit

[Zethson]

Is there an existing module for this?

• I have searched for the existing module

Is there an open PR for this?

• I have searched for existing PRs

Is there an open issue for this?

• I have searched for existing issues

Are you going to work on this?

• If I'm planning to work on this module, I added myself to the Assignees to facilitate tracking who is working on the module

Tasks

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1. Create docker image
2. new module: scsplit/count module #5348
   1 of 2
   new module +1
   
3. scsplit/run module
4. scsplit/genotype module

[IreneRobles]

I am not sure whether I will have time to finish this during the hackathon. However, a bioarpipeline that has an scsplit module, which I am going to use as a template.

https://github.com/theislab/hadge/blob/main/modules/multi/gene_demulti/scsplit.nf

[wxicu]

@IreneRobles hi, you are totally right. The goal is to convert the scsplit module of hadge to nf-core. Please feel free to ask if you have any problems.

[IreneRobles]

Hi @wxicu! Cool! I am almost there. Technically, the scsplit tool should have three tools: genotype, count and run. I am almost there with scsplit/count.

For reference (in case I do not have time to finish this):

• My forked branch where I have been working on scsplit: https://github.com/IreneRobles/nf-modules/tree/scsplit
• My forked branch for the test data: https://github.com/IreneRobles/nf-test-datasets/tree/scsplit
  You will notice that I have a modified version of the test data from the hadge pipeline.

I got the module running and passing tests, what is left is to finish my branch of nf-test-datasets, PR it and link my module tests to that branch. I managed to get a nice docker running scsplit with some help from Simon Murray (dockerfile in my nf-modules repo).

I have drafter a PR here: #5349

[wxicu]

Hi @IreneRobles
cool! I have also added a small dataset for hadge modules to nf-core(https://github.com/nf-core/test-datasets/tree/modules/data/genomics/homo_sapiens/demultiplexing). You can also use this one for testing!