add pangolin 4.3.1 and new version of pdata 1.28; minor CI update

[kapsakcj]

Here's the diff, I upgraded to pangolin-data 1.28 & added a test for a newly designated lineage, LK.1, to the end. Everything else is the same

$ diff pangolin/4.3.1-pdata-1.27/Dockerfile pangolin/4.3.1-pdata-1.28/Dockerfile 
12c12
< ARG PANGOLIN_DATA_VER="v1.27"
---
> ARG PANGOLIN_DATA_VER="v1.28"
189c189,199
< column -t -s, PP218754.1-usher/lineage_report.csv
\ No newline at end of file
---
> column -t -s, PP218754.1-usher/lineage_report.csv
> 
> # new lineage LK.1 that was introduced in pango-designation v1.28: https://github.com/cov-lineages/pango-designation/commit/922795c90de355e67200cf4d379e8e5ff22472e4
> # thank you Luis, Lorraine, Marcos & team from PR Sci Trust for sharing your data!
> # genome on NCBI: https://www.ncbi.nlm.nih.gov/nuccore/2728145425
> RUN datasets download virus genome accession PP770375.1 --filename PP770375.1.zip && \
> unzip PP770375.1.zip && rm PP770375.1.zip && \
> mv -v ncbi_dataset/data/genomic.fna PP770375.1.genomic.fna && \
> rm -vr ncbi_dataset/ README.md && \
> pangolin PP770375.1.genomic.fna -o PP770375.1-usher && \
> column -t -s, PP770375.1-usher/lineage_report.csv

Pull Request (PR) checklist:

• [x] Include a description of what is in this pull request in this message.
• [x] 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 )
• [x] 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)
  • [x] (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
• [x] Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
  • [x] If this README is longer than 30 lines, there is an explanation as to why more detail was needed
• [x] Dockerfile includes the recommended LABELS
• [x] Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• [x] Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

[kapsakcj]

docker build via github actions complained that FROM and as did not have the same casing, so I updated the dockerfile to have FROM x AS app and FROM app AS test to silence the warning.

I also updated the CI check to look for the uppercase AS app and AS test so that it will pass for both casings going forward.

Small/minor update to the CI

[erinyoung]

I am going to

1. merge this PR
2. deploy this to dockerhub and quay using the tag '4.3.1-pdata-1.28'
3. overwrite the 'latest' tag

[erinyoung]

You can check the status of the deploy here : https://github.com/StaPH-B/docker-builds/actions/runs/9670727959

[kapsakcj]

No worries about the CI and thanks for the quick review and deploy!