---
Name: Prokka
URL: http://www.vicbioinformatics.com/software.prokka.shtml
Description: >
	Prokka is a software tool for the rapid annotation of prokaryotic genomes.
---

The Prokka module analyses summary results from the
[Prokka](http://www.vicbioinformatics.com/software.prokka.shtml) annotation
pipeline for prokaryotic genomes.
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 (see below).

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

```txt
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.prokka_fn_snames` to `True` and MultiQC
will instead use the log filename as the sample name.
