[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.