Update samtools in some mulled containers

[nvnieuwk]

No description provided.

[FriederikeHanssen]

What about bwa and bwamem2?

[bgruening]

Is there any new feature in samtools that you need? Please keep in mind that someone needs to pay the bill for those containers

[nvnieuwk]

Not really, just a version bump. I understand if you don't want to submit these because of this

[FriederikeHanssen]

For the mapping mulled containers: there seem to be several bug fixes for dealing with CRAM files and sorting: https://github.com/samtools/samtools/releases/

[bgruening]

Are you hitting those bugs? :)
I just want to raise the issue of environmental impact and cost. So there is a tradeoff. Updating all containers with samtools, with every samtools version is not scalable imho.

An alternative would be that you run samtools as a separate container - which we already provide.

[nvnieuwk]

I'm personally not hitting them, @FriederikeHanssen do you know of anyone having issues?

[bgruening]

That said, if you think the fixes are worthwhile and you need the memory fixes, lets do it. Please just don't do this for the sake of it.

@nvnieuwk If you add too many updates into one container, the CI will time out or we run out of space, you need to create multiple PRs.

[nvnieuwk]

Okay, I'll just remove some of the lesser used containers. We can still add them later if needed. Thanks!

[nvnieuwk]

@bgruening all PRs are done and CI is passing

[nvnieuwk]

@bgruening I fixed the CI failures :)

[bgruening]

Thanks

[nvnieuwk]

Thank you for the merges! The nf-core community will be very happy 🥳

[bgruening]

Your welcome!