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CHANGELOG.md

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Changelog

1.5.0

  • actually remove --force from mamba|conda commands

1.4.0

  • added:
    • bactopia-pubmlst-setup to setup PubMLST REST API connections
    • bactopia-pubmlst-build to build PubMLST databases compatible with mlst Bactopia Tool

1.3.0

  • replace conda/mamba --force with simple rm -rf
    • latest version of mamba removed --force

1.2.1

  • added parallel gzipping of assemblies in bactopia-atb-formatter
  • added size estimation to bactopia-atb-formatter output

1.2.0

  • added bactopia-atb-downloader to download All-the-Bacteria assemblies

1.1.1

  • fixed bactopia-summary not working with Bakta annotations
  • added support for alternative extensions in bactopia-atb-formatter @nickjhathaway 🎉

1.1.0

  • rework bactopia-summary for new AMRFinder+ outputs

1.0.9

  • added bactopia-atb-formatter to format All-the-Bacteria assemblies for Bactopia

1.0.8

  • Fixed bactopia-prepare usage of --prefix not working

1.0.7

  • Fixed bactopia-search not including header name in accessions.txt
  • Added --hybrid and --short-polish to bactopia-prepare

1.0.6

  • Fixed bactopia-summary handling of empty searches

1.0.5

  • Fixed bactopia-download not building prokka and bakta conda envs

1.0.4

  • Fixed bactopia-summary working with new output structure

1.0.3

  • Fixed bactopia-search using missing columns in the query
  • dropped pysradb dependency

1.0.2

  • Added bactopia-datasets to download optional datasets outside of Nextflow
  • consistently use --bactopia-path across sub-commands

1.0.1

Renamed parameter --bactopia to --bactopia-path in bactopia-download

1.0.0

Initial release of the bactopia-py package. This release ports the Python helper scripts from the main Bactopia repo.