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@jvhagey jvhagey released this 02 Jul 22:02
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v2.3.2
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v2.3.2 (07/02/2026)

Full Changelog

Fixed Bugs:

  • Fixed an issue where the UPDATE_PHOENIX workflow crashed when previously failed samples were in the samplesheet (Gitlab Issue # 138).
  • Fixed an issue where UPDATE_PHOENIX would crash if there was no AR gamma file for a sample.
  • Added fix for when BUSCO silently failed, it caused GENERATE_PIPELINE_STATS_WF to be skipped and not produce a synopsis or summaryline files.
  • When an isolate had only poor matches when running ANI and none were above the threshold (minimum of 5 kmer match), sort_and_prep.py would create an incomplete output file, causing a crash. Now, if nothing crosses the threshold, no output file is created and is handled as expected downstream. (Issue # 143)
  • MLST updates:
    • Corrected Providencia stuartii samples to also run under the general Providencia scheme.
    • Fixed DO_MLST subworkflow to handle previously failed samples, related to UPDATE_PHOENIX subworkflow.
    • Added another case to the taxa check section where scoring causing incorrect auto scheme. Citrobacter freundii was found to be identified as Salmonella (Gitlab Issue # 142).
    • Also in Gitlab issue # 142, it showed that some MLST schemes were improperly being displayed in secondary MLST info instead of primary. This has been corrected.
  • GRiPHiN Fixes:
    • Corrected an issue where Acinetobacter baumannii samples that only contained a 'paralog' variant MLST type were being excluded (Gitlab Issue # 141).
    • Fixed an issue where some AR genes were being accidently highlighted as BIG-5 when they were not actually included in that designation (Gitlab Issue # 140).
    • Fixed an issue when running UPDATE_PHOENIX without an outdir that the griphin file would retain empty columns in the AR/HV/PF sections.
    • Fixed an issue where srst2 hits werent coming in for UPDATE_PHOENIX.
    • Corrected labeling check of older griphin version regarding kraken2 columns.
    • Fixed an issue with extra text being pulled through when Shigapass taxonomy is used (Gitlab Issue # 139).

Implemented Enhancements:

  • Added fairy output retention when running UPDATE_PHOENIX.
  • Adjusted how CENTAR, UPDATE_PHOENIX, and CREATE_INPUT_CHANNELS workflows handle input designations internally, input vs indir (No changes to command line options this is just for code cleanup).
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