New module : portello

[sofiademmou]

PR checklist

Add new nf-core module Portello.

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
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• If necessary, include test data in your PR.
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    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
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[famosab]

Few things related to nf-test but looking good!

[famosab]

That is a really large setup for a test. I think its fine but I would argue that one could generate the input file once and store it in test-datasets so that we do not compute it all the time :)

[sofiademmou]

Thank you so much for your review !

I applied all your suggestions but I had a small question for this one (since I am pretty new to nextflow and nf-core I was not sure how to proceed) :
would it be better to generate and store only the assembly (result of HIFIASM) and keep the rest of the setup, so other people could use this file in other modules if needed ? Or should I generate and store the files I need for this module (results of MINIMAP2_ALIGN and PBMM2_ALIGN) even if it would only be used for this ?

[famosab]

I would say it depends on the size, but my gut is usually that if you need many many setup steps that this is just a waste of compute. How big would these files be? I think we can justify storing them even if its just for the module. Did you check if there are no files that would fit your purpose?

[sofiademmou]

I see ! I would have to add 2 bam files and their index, the biggest file would be 54kb. I think that's reasonable, right ?
The setup for portello is pretty specific so I haven't found any files that I could use.

[famosab]

I would put the val output_vcf also in the one input tuple :)

[sofiademmou]

Ok ! I'll add it so we have only one input tuple ! :)

[famosab]

But if you think that both the assembly mode and the output_vcf is not something you would decide on a per sample basis I think we can also put them into their own inputs. This whole input thing is something that I became a bit torn on what way would be the best way forward :)

[sofiademmou]

I think the assembly_mode should definitely be on a per sample basis, but I wasn't sure for the output_vcf. But I think it makes sense for it to be dependent on the sample, so I will leave it all in one input tuple as you suggested ! :)