[theiaprok] upgrade amrfinderplus to latest version that includes stxtyper & db update

[kapsakcj]

🆒

📌 Explain the Request

This is low priority and requested by myself, though I'm confident our users would also want to stay up-to-date with the latest amrfinderplus version and database version

staph-b just deployed the docker image for the latest version of amrfinderplus that includes stxtyper: StaPH-B/docker-builds#1096

https://hub.docker.com/r/staphb/ncbi-amrfinderplus/tags

stxtyper is run when the option amrfinder -O Escherichia is used. It should produce results identical to the standalone task for stxtyper. The stxtyper versions are slightly different (v1.0.27 in amrfinderplus docker vs 1.0.24 in stxtyper docker image) but the underlying algorithm has not changed.

amrfinderplus v4.0 changes detailed here: https://github.com/ncbi/amr/wiki/New-in-AMRFinderPlus We may need to be careful about parsing of output TSV as some column headers have changed.

I ran a quick test with the new docker image and TheiaProk_Illumina_PE, and it ran successfully ✅ but I didn't thoroughly check the TSV parsing functionality. So that needs to be checked during the upgrade.

[kapsakcj]

the latest version is now v4.0.3 and db version 2024-12-18.1

more info on the staphb docker image can be found here: https://github.com/StaPH-B/docker-builds/tree/master/build-files/ncbi-amrfinderplus/4.0.3-2024-12-18.1

[kapsakcj]

Let's wait until the next amrfinderplus version (v4.0.15) is released. It should be released very shortly and we'll get it added to staphb's docker images. I'll ping back here when the docker image is ready for us to copy to GAR and update the default in the WDL

EDIT: version has been released https://github.com/ncbi/amr/releases/tag/amrfinder_v4.0.15

[kapsakcj]

New docker image has been copied to our GAR: us-docker.pkg.dev/general-theiagen/staphb/ncbi-amrfinderplus:4.0.15-2024 -12-18.1

This version of amrfinderplus (4.0.15) now includes stxtyper v1.0.31. It would be good to add a bit of code and a new output string to capture the stxtyper version stxtyper --version (or see stxtyper task for code on how I capture it there). This would be an optional output that would only apply if using amrfinder --plus --organism Escherichia flags, so perhaps only capture when that is run, but otherwise don't capture it.

Again, since this is a major upgrade of amrfinder from v3.x.x to 4.x.x, we should double check output column parsing to ensure it's still behaving the way we want it to.

[kapsakcj]

FYI @AndrewLangvt , just making sure you get a notification for this. This request is ready to be worked on

[kapsakcj]

aaaand there's another version just released: https://github.com/ncbi/amr/releases/tag/amrfinder_v4.0.19

not critical to upgrade to this version (we don't have a staphb docker image for it just yet) as the changes were pretty minor.

But just wanted to note in case we do want to be absolutely up-to-date with the current version

[kapsakcj]

OK new docker image is now available: staphb/ncbi-amrfinderplus:4.0.19-2024-12-18.1

https://hub.docker.com/r/staphb/ncbi-amrfinderplus/tags

I have not copied to our GAR, but it's ready for usage