This component performs annotations using the annotations available in prokka.

Input/Output type

  • Input type: fasta
  • Output type: None


  • Although the component doesn’t have an output channel it writes the results into the publishDir.


  • centre: sets the center to which the sequencing center id. Default: ‘UMMI’.
  • kingdom: Selects the annotation mode between Archaea, Bacteria, Mitochondria, Viruses. Default: Bacteria).
  • genus: Allows user to select a genus name. Default: ‘Genus’ (same as prokka). This also adds the use of the –usegenus flag to prokka.

Published results

  • results/annotation/prokka_<pid>/<sample_id>: All the outputs from prokka will be available in these directories.

Published reports


Default directives

  • prokka:
    • cpus: 2
    • container: ummidock/prokka
    • version: 1.12