Modules for scrnaseq about scrnaseq HOT 12 CLOSED

PRs for kallistobustools/ref and kallistobustools/count are also up and passing all tests. Thanks, @KevinMenden for the quick reviews!

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Buried in projects at the moment, sorry folks for not being as responsive as during the hackathon :-(
Will try to catch up once I'm a bit freed up again

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I just checked what is still missing, I think there is an open PR for kallisto/quant here:
nf-core/modules#351
So no need to do that again. Will have a look later and see what's missing there.

I think the build_gene_map might be best to implement as a local process, what do you think?
I have modified the gffread module to handle the txp2gene thing, so I checked that off as well.

STAR and samtools should be possible via available modules, right? 🤔
Then it would be just alevin_qc and the kallisto/bustools modules left. I can have a go at alevin_qc now. Is kallisto bus and bustools not already implemented by the kb module in a way?

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yes, we will not need kallisto bus and bustools for now as the kb modules are there

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Made a draft PR for salmon alevin here: nf-core/modules#397
So I checked it off the list. Works locally with some test data but that's too big for uploading so I'm keeping that as draft for now until we know about what we'll use as scRNA-seq test data.

Next would be alevinQC to complete the alevin stuff - but that uses a script in bin and we are not really supporting this properly with modules, so that may be a good candidate for a local module?

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Sorry for the delay with this PR nf-core/modules#351. I've been swamped with work in the lat couple of weeks. I'll get it done and ready for review in the weekend, is that alright? If you need it sooner, I can work on it tonight.

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Hi @BatoolMM, sometime next week would be awesome, but not need to stress yourself, there are enough other modules/things to finish 👍

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Would be nice to turn all remaining local modules into nf-core modules before the next release!

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Doesn't look like we need these anymore: Kallisto + Bustools are now handled by that python wrapper app (kbtools), which means we won't have to add additional modules to nf-core/modules apart from that (which is already there).

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There's still a bunch of local modules, though. Would be nice if as many of those as possible could be replaced with modules from the modules repo.

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Yeah fair enough
Could move these upstream 👍🏻

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Closing in favor of #264

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