Something to discuss. We have many modules that use meta.single_end to determine whether they are single end or not. I know that some people have strong feelings on whether this should be done, or whether the module is better served by just checking the number of input files https://github.com/nf-core/modules/pull/9585#discussion_r2694659644

The number of input files is not a perfect determiner of single-endedness as you can have interleaved read files

(even if I hate interleaved files) Also if you really want to go down the route of having the computer check, then we should be having checks that it's not exceeding 2 or more. Also I hate having groovy checking stuff because of the weird thing where if it gets a single element it'll just 'split' by

/

for you without asking

interleaved files are a much more sensible file format than our horrible coupled two file R1/R2s, but that is a separate issue 😉

We store all our raw reads in unaligned CRAM format, which tracks the mate information as a SAM flag 😎

#C0749PAEU9F

single_end

should be an input value of the module 😉

Agreed! Record types will fix it all 😎

It's basically in the guidelines, but for legacy reasons we make an exception for

single_end

as you can have interleaved read files

or 3 files, or 4 files. Or more! At my old company: R1 = forward R2 = UMI R3 = reverse R4-n = other stuff

And don't look at tools like adapterRemoval 😬