adding kaptive version 3.0.0b1

[erinyoung]

There's a new version of kaptive!

I think it's mainly for documentation changes (https://github.com/klebgenomics/Kaptive/releases/tag/v2.0.9)

I just copied 2.0.8 and changed the software version arg.

Update 2024-05-14
Since version 3.0.0b1 came out, I've decided to skip 2.0.9. Version 3.0.0 is very different from prior versions.

This is now ready for review.

Pull Request (PR) checklist:

• Include a description of what is in this pull request in this message.
• The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15 )
• Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number (i.e. spades/3.12.0/Dockerfile)
  • (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
• Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
  • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
• Dockerfile includes the recommended LABELS
• Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

[erinyoung]

Converting to draft because Kaptive version 3.0 came out

[erinyoung]

There are quite a few changes with this new version.

1. The Vibrio database from https://github.com/aldertzomer/vibrio_parahaemolyticus_genomoserotyping is no longer compatible, which is actually why I was using kaptive, so this makes me very sad
   • The lines for this database are still included, they are just commented out with the hope that they'll be included again later
2. The dependencies have changed. blast is no longer needed, but minimap2 is (not listed anywhere)
3. Requires python version 3.9 or higher, so I changed the base image to 3.9-slim
4. The executable has changed
5. How the executable is used has changed

I've updated the tool-specific readme to reflect these changes.

[erinyoung]

Closing this PR until the Vibrio database is updated