One species is enough

• removed duplication of species file in results files used to generate report. Addresses #194

Full Changelog: v3.6.3...v3.6.4

Fixing dependency on column names for amr/plasmid collation

Recent updates to amrfinderplus and abritamr resulted in the incorrect column names being used. Added in flexible option to be backwards compatible with previous versions of these tools. Addresses issue #192

Full Changelog: v3.6.2...v3.6.3

Preview mash magic

• added conditional functionality to address different settings for using mash on reads vs assemblies issue #188

Full Changelog: v3.5.2...v3.6.1

Added gtdb syntax consistency

• added capability to use gtdb syntax ie Enterococcus faecium_B for abritamr and potential serotyping (issue #187 )

Full Changelog: v3.5.1...v3.5.2

Cleaning up

• fixed up gubbins env
• bug fix for comment in report

Full Changelog: v3.5.0...v3.5.1

Housekeeping help

• implemented some changes to installation process to address #171 #170 #172
• made kraken2 database and mlst databases dependencies of the the workflow - so that any changes to these resources will trigger a rerun of these processes. In part address #183
• added checks for mobsuite and ectyper database installation - network drop outs may hide that these are not complete issue #181 #180
• tidied up command line options removing some legacy code #185
• filtering contigs length issue #184
• updated dependency ska env yaml - pinned pandas <3.0 to prevent issue with ska distance

Full Changelog: v3.4.3...v3.5.0

Squashing some persistent bugs

• finally fixed the -h bug #169
• sped up prokka #176
• made cluster table visible when only one threshold (not heirchical) #167
• changed tests --cpus in CI to make testing quicker

What's Changed

• Speed up prokka annotation step with --noanno by @Copilot in #177

Full Changelog: v3.4.2...v3.4.3

Match making species

• address #174 fixed input to detect species for use in abritamr -> amrfinder

Full Changelog: v3.4.1...v3.4.2

Bugfix for mixed run of AMR and Typing

• updated CLI for preview with the settings set for prokka and speciation off by default
• modified path of input data through workflow to ensure that assemblies from reads and supplied assemblies move through the pipeline to address issue #168
  Full Changelog: v3.4.0...v3.4.1

Quick preview mode added

• added in a preview mode bohra run preview --help which will run mash and generate a NJ tree for quick assessment of dataset.
• prokka can be slow - made an option to turn this off (off by default when using preview)
• updated environment files to pin updated lissero, meningotype and ngamster with fixed pkg_resources issues
• pinned new version of mlst (>= 2.32.2) to provide additional information on mlst

Full Changelog: v3.3.0...v3.4.0