Can I please get a review? It is a small one.

To be honest, I don't think that subworkflows that are align + stats are worthwhile. That is something that we've discussed in the <!subteam^S044DU0NG68> recently

Yeah, I agree. This is a way too common pattern, but if each possible aligner has it’s own subworkflow it kind of loses it’s purpose

yeah, I vote for reaping stats out of most subworkflows

I’d go the other way around 😅 I we really want a subworkflow, make one that supports all aligners and dump the stats stuff in there. Have our cake and eat it too

See @Evangelos Karatzas's mega preprocessing subworkflow ;)

-> nf-co.re/subworkflows/fastq_shortreads_preprocess_qc

Screenshot_20260708-151920.png

Dang. Is that used somewhere?

I want my subworkflow to be small as possible

xzibit

Also, that’s fastq processing, not aligners 😅

Never said it was ,but concept is the same

I remember @Júlia Mir wanted to introduce module classes for this reason, not sure where that discussion stands right now

Currently it seems like all different aligners have a separate subworkflow (maybe because of output differences?). What if we could have short read and one long read sub workflow with all aligners suitable for for each data type? and then as @Matthias De Smet suggested throw in stats too