v2.1.7

v2.1.7

• add more messages of the day

v2.1.6

v2.1.6

• fix missing_required being overwritten to false when no reads are found for Bactopia Tool inputs
• simplify read-check conditions to use already-resolved input values

v2.1.5

v2.1.5

• refactor scrubber input validation into validateScrubberParams helper to reduce duplication
• add --deacon_db validation for the scrubber workflow

v2.1.4

v2.1.4

• refactor database path validation into validateDbPath helper to reduce duplication
• add --traitar_db validation for the traitar workflow

v2.1.3

v2.1.3

• check --nohuman_db and --use_srascrubber are not both null/false
• improve test coverage

v2.1.2

v2.1.2

• test floats as strings are actually floats

v2.1.1

v2.1.1

• changed bactopia URL from https://bactopia.github.io/ to https://bactopia.io/

v2.1.0

v2.1.0

• Bump minimum Nextflow version to 26.04.0

v2.0.3

v2.0.3

Added

• Added new Message of the Day joke

Fixed

• Added header validation to processFOFN() and processAccessions() — both now check that the first line contains all required columns before processing data rows
  • processFOFN() requires: sample, runtype, r1, r2, se, ont, assembly, genome_size, species
  • processAccessions() requires: accession, runtype, species, genome_size
  • Missing columns produce a clear error listing found vs expected columns and suggest using bactopia prepare or bactopia search to generate properly formatted files
• Fixed SE/ONT read detection in BactopiaTools._collectInputs():
  • SE reads now use {sample}_SE.fastq.gz instead of {sample}.fastq.gz
  • ONT reads now use separate {sample}_ONT.fastq.gz file path
  • ONT detection changed from checking for NanoPlot HTML report to ont.txt marker file
  • PE read detection now correctly excludes ONT samples
• Fixed JsonSchemaValidator rejecting string "true"/"false" values for boolean parameters — CLI arguments arrive as strings, so the validator now accepts these as valid booleans

v2.0.2

v2.0.2

Fixed

• Fixed --help_all crashing with GroovyRuntimeException by casting params["help_all"] to Boolean before passing to HelpMessageCreator constructor (CLI params arrive as strings)