ENH: add filter-reads-kraken2 action

[misialq]

Description

This PR introduces a new action filter-reads-kraken2 that allows filtering a set of reads using their corresponding Kraken2 classifications.

• Taxonomy can be provided either as a literal (e.g., "Bacteria") or as an ID integer (e.g., "2").
• It is possible to filter only the indicated taxonomy or also include all of its descendants (default).
• It is possible to toggle what is being retained and discarded (by default the reads of indicated taxonomies will be retained).

AI Disclosure

• NO AI USED.
• AI USED.

AI Usage Details

Codex was used during early stage implmentation. All the code was reviewed and tested before PR submission.

[codecov]

Codecov Report

❌ Patch coverage is 93.29609% with 12 lines in your changes missing coverage. Please review.
✅ Project coverage is 94.52%. Comparing base (1b6627a) to head (a2209ae).
✅ All tests successful. No failed tests found.

Files with missing lines	Patch %	Lines
q2_annotate/kraken2/filter_reads.py	93.10%	6 Missing and 6 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #340      +/-   ##
==========================================
- Coverage   94.60%   94.52%   -0.09%     
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  Files          35       36       +1     
  Lines        2669     2848     +179     
  Branches      397      434      +37     
==========================================
+ Hits         2525     2692     +167     
- Misses         72       78       +6     
- Partials       72       78       +6     

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[VinzentRisch]

I will review this on monday, if that is okay. I want to finish something today.

[VinzentRisch]

Hey Michal
I ran the code with the data from the mock tutorial and with a couple of querys.
It all looks good but I have two comments below:

[VinzentRisch]

Yes looks good!