Taxonomic classification is completed using Mash (DEFAULT; mash_screen.nf), or Kraken2 (OPTIONAL, or when samples are flagged metagenomic; kraken.nf). Species classification and subsequent subtyping can be skipped by passing --skip_species_classification true on the command line. To select Kraken2 for speciation rather than mash add --run_kraken true to your command line arguments.
Input
Contig file (fasta) from the FinalAssembly dir
This is the final contig file from the last step in the CleanAssemble workflow (taking into account any skip flags that have been used)