@Matthias De Smet I seem to remember you are a fan of massive modules update 😆. I am looking at https://github.com/nf-core/modules/pull/12983/ which adds gzip has a dependencies on some modules, there was a way via wave to change the base layer, right and have gzip there by default?

Yes! Containers need to be created through the seqera wave API or you need the use a slightly modified version of #CE5LG7WMB (PR pending approval) github.com/nf-core/tools/pull/4449

I don't understand why the base wave image doesn't have gzip

While we're at it. I see that here, this PR add strandness as an input for modules/nf-core/sentieon/rsemcalculateexpression/main.nf I'd rather we keep that in args, similarly to how we did it in https://github.com/nf-core/rnaseq/pull/1913/ cc @Jonathan Manning what is your take on this ? (as I saw you approved and merged said PR) And maybe we need to document this properly, or add strandeness as an official field

that’s the thing, the docker image does, but the singularity image doesn’t. I wanted to pin it to the

conda-forge

version to avoid any drift, but Paolo wasn’t a fan 🤷🏻

My opinion is that strandedness should be an official field

Can we maybe split these three topics in a separate thread so answers don’t get buried? 😅

sorry

this PR add strandness as an input for modules/nf-core/sentieon/rsemcalculateexpression/main.nf

Yeah, that's clearly wrong, it's not mandatory I think

My opinion is that strandedness should be an official field

I was happy enough when that was the situation too, don't really understand why we had to strip it, been dealing with some fallout of that this week