v0.3.0

Added

• Isolate single sample reports
• Include disinfectant resistance results in the report.
• MLST core gene analysis added to --isolates parameter.

Changed

-species parameter is removed, valid pointfinder species will be inferred from MSLT results.

• In case flye fails due to low coverage, the workflow will continue and this will be indicated in the report.
• Bumped minimum required Nextflow version to 22.10.8
• Enum choices are enumerated in the --help output
• Enum choices are enumerated as part of the error message when a user has selected an invalid choice

Fixed

• Replaced --threads option in fastqingress with hardcoded values to remove warning about undefined param.threads