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v2.2.1

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@jvhagey jvhagey released this 13 Apr 20:58
· 194 commits to main since this release
v2.2.1
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Learn about vigilant mode.

v2.2.1 (04/13/2026)

Full Changelog

Fixed Bugs:

  • MLST Fixes
    • Corrected hard stop when an Enterobacter isolate is in the analysis. There was a change to the named folder from processing pubMLST data.
    • Corrected the missing Serratia entry in the local_MLST_converter to match up the srst2 database assignment.
  • For --mode SRA or --mode CDC_SRA created fall back to use SRR number if metadata for sample_name is not in ncbi metadata.
  • Fixed Terra specific bug #197.
  • Fixed bug that caused failure of CHECK_SHIGAPASS_TAXA step #196.
  • Fixed error when BBDuk was run with memory flag it was incorrect passing an extra dash ('-') to the tool

Implemented Enhancements:

  • --mode SRA and --mode CDC_SRA allow ERR numbers as well as SRR.
  • Added --mode COMBINE_GRIPHINS to pass several griphin scripts to the pipeline to combine into one griphin report.
  • Added gamma plasmidfinder to tools run during --mode update_phoenix.
  • Added better version tracking and gamma plasmidFinder changes to the updater_log in --mode update_phoenix
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