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@sylvinite sylvinite released this 15 Apr 11:42
· 892 commits to master since this release
v2.3.25
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Learn about vigilant mode.

Bioinformatics:

  • Logging is now more explicit and generates more 'task complete' text files, to more easily keep track of how a project is doing.
  • Both e-mail and custom configuration can now additionally also be provided directly on the CLI
  • README and configExample updated to both contain more useful info; and to be more readable
  • Basic installation script install.sh now streamlines creation of microSALT instances a lot
    --no_update flag added as to not waste time by unnecessarily check pubMLST for updates
  • microSALT now resolves symlinks, as to not falsely report a project exists despite “dead links”
  • microSALT can now handle external/customer project names quite well, making research projects easier to reanalyze.
  • microSALT now also reports in json format, primarily for microSALT<->Vogue interaction
  • Functionality for internal ST management added under util -> resync

End-user:

  • Novel ST are stored under temporary ST (so called [I]nternal ST). microSALT tracks the upload status of these samples.
  • Control samples are now a lot more extensively gathered; and now have the threshold ‘-‘.
  • microSALT can generate resistance overview report (csv format)
  • microSALT logotype displays correctly
  • There is no longer a case where ‘hits below threshold’ are displayed
  • Unidentified organisms now default to written name

Internal:

  • All jobs (including sample) are now based on the project function, with variations.
  • Resistance "Type" is now automatically resolved instead of basing it on notes.txt
  • Database indexation is a lot more foolproof
  • Added very very basic travis CI support
  • Added customer id/name tracking
  • Replaced BLASTs internal top-filter with manual filter to guarantee best hit.
  • microSALT now correctly reassigns externally-added organisms as pubMLST ones, if they are found in the latter at a later stage
  • microSALT now handles the data page of pubMLST correctly again
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