Add srst2 0.2.0 with custom Vibrio cholerae database

[cimendes]

Motivation

This PR adds a custom vibrio database to the srst2 0.2.0 container with sequences used for in silicon typing. It contains minimal alterations and the description of the database has been added to the README file.

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

[kapsakcj]

I suggest that we set this PR as draft until we test the container on more V. cholerae samples. Just want to put this container through more extensive testing before merging the PR here.

I've pushed the docker image to my personal quay repo that we can use for testing in Terra: https://quay.io/repository/kapsakcj/srst2?tab=tags

docker image name quay.io/kapsakcj/srst2:0.2.0-vcholerae

[kapsakcj]

Everything looks great as far as README.md changes go and the dockerfile itself.

GHActions test worked as expected, including the V. cholerae test sample as having hits to the expected ctxA, ompW, tcpA_ElTor, toxR, and wbeN O1 markers.

Further tests done in Terra (not shown here), also show concordance between expected phenotypes (PCR positivity) & in silico detection via srst2 approach

I will now deploy this to dockerhub & quay the the docker image name and tag: staphb/srst2:0.2.0-vcholerae. I will also overwrite the staphb/srst2:latest tag on dockerhub & quay.

Thank you!

[kapsakcj]

you can view the deployment workflow progress here: https://github.com/StaPH-B/docker-builds/actions/runs/4621877426

I expect the docker images will be available on dockerhub & quay in the next 15 min or so