v1.7.0

1.7.0

• bactopia-download
  • Use appropriate executable for singularity and apptainer
  • support Bactopia v4
• bactopia-workflows will print the path for a specific Bactopia wf
• bactopia-merge-schemes will merge schemes and configs for a given wf

Full Changelog: v1.6.1...v1.7.0

v1.6.1

1.6.1

• shuffle ncbi related module out of utils and into ncbi
• fixed missing import in bactopia-prepare

v1.6.0

1.6.0

• bactopia-search
  • fixed issue when no tax id is associated with an accession
  • NCBI genome size is now optional (--use-ncbi-genome-size)
  • moved modules to specific database files
• Remove executor dependency

v1.5.1

1.5.1

• fix ena metadata parsing in bactopia-search to handle missing columns

v1.5.0

1.5.0

• actually remove --force from mamba|conda commands

v1.4.0

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

v1.3.0

1.3.0

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

v1.2.1

1.2.1

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

v1.2.0

1.2.0

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

v1.1.1

1.1.1

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