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@jvhagey jvhagey released this 15 May 02:34
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v2.3.0
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v2.3.0 (05/14/2026)

Full Changelog

Fixed Bugs:

  • Fixed bug that caused failure for --mode combine_griphins when only 2 griphins are passed.
  • Fix for null being string when run on Seqera Cloud and MLST E. coli methods applied to Shigella as well. Thanks to @DOH-HNH0303 for the PR.
  • MLST Fixes:
    • Corrected Mycobacterium abscessus linkage for SRST2 lookup.
    • MLST now called correctly for Serratia species issue 206

Database Updates:

  • Hypervirulence database underwent a major overhaul and now contains 281 sequences. The 5 hypervirulence genes were extracted from NCBI Klebsiella pneumoniae Refseq genomes using hypervirulence reference sequences from the GCA_056237995.1 genome. Resulting hypervirulence sequences were deduplicated and checked for nonsense mutations, start and stop codons. Sequences with internal stop codons, no start or stop codon were excluded. Since these sequences were in silico based, their functionality has not yet been confirmed.
  • Updated remaining databases as usual:
    ResGANNCBI: 20260430 for gamma_AR and srst2_AR
    amrfinderdb: 20260324 for amrfinder+
    • Version 2026-03-24.1
      MLST: 20260504 for MLST and SRST2_MLST
      PF_Replicons: 20260430 for gamma_PF
      Assembly_stats: 20260430 for assembly_ratio and gc_content
      names & nodes: 20260430 for kraken2 and determine_taxid

Implemented Enhancements:

  • `--mode update_phoenix' now properly handles when previous runs were of the scaffold/cdc_scaffold types
  • Added gamma hypervirulence to tools run during --mode update_phoenix.
  • Added unzipped filtered scaffolds and contigs to Terra.bio output as requested in issue 204.
  • Bash scripts were converted to python for cohesiveness including, afterSpades.sh, calculate_assembly_ratio.sh, determine_taxID.sh, fairy_proc.sh, kraken2_best_hit.sh, pipeline_stats_writer.sh and sort_and_prep_dist.sh.
  • Old scripts no longer in use were remove including, beforeSpades.sh, getMLST2_phoenix.py, pipeline_stats_writer_trimd.sh, dumpsoftwareversions_mod_with_out.pyand to_json.py.

Container Updates:

  • Containers updated to include developers bug fixes:
    • amrfinderplus: v4.2.5 to v4.2.7

Contributors

DOH-HNH0303
Assets 3
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