Determine Species

subworkflows/local/determine_species

Steps

1. 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.

IMPORTANT: If species specific subtyping tools are to be executed by the pipeline Mash must be the chosen classifier

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)

Output

• Assembly
  • PostProcessing
    • Speciation
      • MashScreen