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adding gfastats version 1.3.9 #1210

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There's a new version of gfastats!

According to the release notes, this version fixes a bug introduced in 1.3.8 (which we sort of skipped in our repo).

Other notes: --seq-report is no longer a supported flag. I imagine this update will break any workflows that use it. Due to this change, I had to adjust the test to use the --segment-report flag instead.

I copied the files from 1.3.7, updated the version arg, changed the CMD line to json format, and updated the test to reflect current usage.

$ diff build-files/gfastats/1.3.7/Dockerfile build-files/gfastats/1.3.9/Dockerfile 
1c1
< ARG GFASTATS_VER=1.3.7
---
> ARG GFASTATS_VER=1.3.9
3c3
< FROM ubuntu:jammy as app
---
> FROM ubuntu:jammy AS app
37c37
< CMD gfastats --help
---
> CMD ["gfastats", "--help"]
41c41
< FROM app as test
---
> FROM app AS test
55c55,56
<   gfastats --tabular --seq-report gfastats-${GFASTATS_VER}/testFiles/random6.circular.gfa
---
>   gfastats --tabular --segment-report gfastats-${GFASTATS_VER}/testFiles/random6.circular.gfa > results.txt && \
>   head results.txt

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)
    • (optional) All test files are located in same directory as the Dockerfile (i.e. build-files/shigatyper/2.0.1/test.sh)
  • Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. docker-builds/build-files/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

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