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