neissflow v2.1.0

• update snippy args to accomodate high recombination regions
• lowered presence absence threshold for plasmid genes
• updated mtrR promoter SNP reporting format
• added strandedness check for depth reporting
• reformatted repo structure
• migrated to nf-core 3.3.2
• updated databases
• included new database update script and instructions
• bug fixes
• swapped RAxML 8 for RAxML-NG
• added contigs for testing
• fixed test profiles
• updated docs

neissflow v2.0.1

• Removed references to Nextflow parameters within modules
• Swapped out Snippy container for one without SnpEff version bug

neissflow public release

v2.0.0 is the first public release of neissflow. Version 1.0.0 was available for internal CDC use only. This version update brought the pipeline up to nf-core standards, eliminated redundancy, and incorporated new functionality.