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Prokka

note

Rapid annotation of prokaryotic genomes.

http://www.vicbioinformatics.com/software.prokka.shtml

The Prokka module accepts two configuration options:

  • prokka_table: default False. Show a table in the report.
  • prokka_barplot: default True. Show a barplot in the report.
  • prokka_fn_snames: default False. Use filenames for sample names (DEPRECATED - use global use_filename_as_sample_name instead).

Sample names are generated using the first line in the prokka reports:

organism: Helicobacter pylori Sample1

The module assumes that the first two words are the organism name and the third is the sample name. So the above will give a sample name of Sample1.

If you prefer, you can set config.use_filename_as_sample_name to True and MultiQC will instead use the log filename as the sample name.

File search patterns​

prokka:
  contents: 'contigs:'
  num_lines: 2