## Genomic annotation

`rule prokka`

```{r prokka, echo = F, message = F, warning = F, error = T}



prokka_summary = read_delim(glob_list$prokka, id = "file", comment = "#", col_names = c("name", "value"), delim = ": ") %>%
    select(file, name, value) %>%
    filter(name != "organism") %>%
    filter(str_detect(value, "\\d")) %>%
    mutate(
        sample = basename(file) %>% str_remove("\\.txt$"),
        value = as.numeric(value)
    ) %>%
    pivot_wider(id_cols = sample, values_fill = 0)


metadata_translate %>%
    select(sample) %>%
    left_join(prokka_summary, by = "sample") %>%
    custom_dt("prokka")


```

*Table `r tableno()`: Overview of the number of different gene types. Called using the [Prokka](https://github.com/tseemann/prokka) genome annotator.*

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