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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.

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