adding augur version 32.1.0

[erinyoung]

There's a new version of augur!

According to the release notes there are some new features and bug fixes.

I copied the files from 32.0.0 and updated the version args for augur and seqkit.

The full diff:

$ diff build-files/augur/32*/Dockerfile
3,4c3,4
< ARG AUGUR_VER="32.0.0"
< ARG SEQKIT_VER="2.10.1"
---
> ARG AUGUR_VER="32.1.0"
> ARG SEQKIT_VER="2.12.0"

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/build-files/samtools/1.15 )
• Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number in build-files (i.e. docker-builds/build-files/spades/3.12.0/Dockerfile)
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  • 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
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[kapsakcj]

should be changed to --output-sequences results/filtered.fasta as --output is deprecated and will be removed in the next major release

[erinyoung]

Is this only the case with augur filter? Or are there others that need to be updated too?

[kapsakcj]

I think so, yes. I was going off of warnings in the the original github actions workflow and they have disappeared after your latest commit. Thanks for changing that!

[kapsakcj]

Tests passed, just have one request for altering an output flag for the augur filter. Also request that the versions of dependencies in the readme are updated to reflect what was installed via pip

[erinyoung]

I have updated the readme with the updated dependency versions, which now includes a full list of dependencies installed via pip in a dropdown. I also updated the usage in the README to reflect the same usage of augur filter which is used in the test stage.

[kapsakcj]

thanks for making those changes I requested 👍 LGTM

[kapsakcj]

Thanks for the PR! Deploy workflow here: https://github.com/StaPH-B/docker-builds/actions/runs/20784583257