new module Bakta

[louperelo]

Bakta is a tool for rapid and standardized annotation of bacterial genomes, MAGs and plasmids. We are using Bakta as one of the annotation tool options in nf-core/funcscan and would like to include its output in the pipelines MultiQC report.

• This comment contains a description of changes (with reason)
• CHANGELOG.md has been updated
• There is example tool output for tools in the https://github.com/ewels/MultiQC_TestData repository: #258
• Code is tested and works locally (including with --lint flag)
• docs/README.md is updated with link to below
• docs/modulename.md is created
• Everything that can be represented with a plot instead of a table is a plot
• Report sections have a description and help text (with self.add_section)
• There aren't any huge tables with > 6 columns (explain reasoning if so)
• Each table column has a different colour scale to its neighbour, which relates to the data (eg. if high numbers are bad, they're red)
• Module does not do any significant computational work

[louperelo]

Thank you for the review @vladsavelyev! Please check if I resolved the merge conflict for the CHANGELOG.md and README.md correctly.

[vladsavelyev]

But it's not a percentage? Also, I don't think {:i} is a recognised format string. At least it doesn't seem to work, as numbers are displayed in the table as string (you can tell that by the lack of thousand groups separators!). I'll change them to "{:,d}" if that's okay.

[vladsavelyev]

@louperelo - thanks for responding to the review quickly! Last time I didn't complete it, just left a few quick suggestions 😅 Now it's done. I mostly merged my suggestions directly into the branch, hope it's okay. Here is what I changed:

• fixed the format strings to "format": "{:,d}"
• table colors - I tried to make them match similar metrics in the QUAST module, plus added a shared_key: gene_count for the CDS count to make the number scale comparable with QUAST
• got rid of spaces in the metric keys - it's not a problem for MultiQC, but theoretically might be some downstream tools that might use MultiQC output
• iterating over f["contents_lines"] to avoid extra splitting
• in search patterns, removed num_lines: 26 to make it more future-proof

[ewels]

LGTM, thanks!