Update medaka to version 2.0.0

[erinyoung]

Medaka now has a cpu-only version. This image should be much smaller than the one ONT maintains on dockerhub.

I updated the base image and several more features from the 1.2.0 version.

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]

Closes #734

[Kincekara]

Thank you for putting all these together! There is a lot of work here.

[Kincekara]

Deploy link: https://github.com/StaPH-B/docker-builds/actions/runs/11163100121