adding medaka version 1.11.2

[erinyoung]

Instead of using the older Dockerfiles for medaka, I copied the artic version 1.24-1.11.1 Dockerfile and just removed all the artic lines.

The prior medaka Dockerfile is for version 1.2.0, which was three years ago. This means that I needed to create an app and test stage in the Dockerfile and a README.md for 1.11.1. For the test, I downloaded an assembled CRPA genome with its corresponding nanopore reads.

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

[erinyoung]

Medaka 1.11.2 came out, so I've updated the version number.

I did attempt to use the nvidia/cuda:11.2.2-cudnn8-runtime-ubuntu20.04 base (focal) like nanopore does for their version of medaka, but I kept running into issues with git lfs and pyapboa.