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Fix 2 bugs in SRST2 #6493

Merged
merged 4 commits into from
Oct 28, 2024
Merged

Fix 2 bugs in SRST2 #6493

merged 4 commits into from
Oct 28, 2024

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hexylena
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FOR CONTRIBUTOR:

  • I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • License permits unrestricted use (educational + commercial)
  • This PR adds a new tool or tool collection
  • This PR updates an existing tool or tool collection
  • This PR does something else (explain below)

Fixes #6487
Fixes #6459

The collections are also separated because it made them very difficult to use in an automated way, especially with hamronize.

Either they're a separate collection or you have to

  • extract element identifiers (txt,tabular formatted output due to SRST2 has incorrect format on discover datasets outputs. #6459 prevents this tool from selecting this collection weirdly)
  • select matching element identifiers
  • filter collection (because it won't let you just .. grep. you have to specify the precise list of identifiers. I get it, but the UX isn't great.)

@hexylena hexylena mentioned this pull request Oct 28, 2024
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bgruening
bgruening approved these changes Oct 28, 2024
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Great, thanks @hexylena!

@hexylena

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@hexylena hexylena merged commit 90275e5 into main Oct 28, 2024
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@hexylena hexylena deleted the anaconda-rooster branch October 28, 2024 13:00
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@bgruening bgruening bgruening approved these changes

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SRST2 MLST regex incorrect SRST2 has incorrect format on discover datasets outputs.
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@hexylena @bgruening