Gtdbtk

Bug Fixes:
* (475) If all genomes are classified using ANI, Tk will skip the identify step and align steps

Minor changes:
* Add hidden '--skip_pplacer' flag to skip pplacer step ( useful for debugging)
* Improve documentation
* Convert stage_logger to a Singleton class
* Use existing ANI results if available

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Bug Fixes:

* Fix prodigal_fail_counter issue

Bug Fix:

(471): Fix pplacer issue

* (470) Add missing Pydantic dependency.

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Minor changes:

* (433) Added additional checks to ensure that the `--outgroup_taxon` cannot be set to a domain (`root`, `de_novo_wf`).
* (459/ 462 ) Fix deprecated np.bool in prodigal_biolib.py. Special thanks to neoformit for his contribution.
* (466 ) RED value has been rounded to 5 decimals after the comma.
* (451 ) Extra checks have been added when Prodigal fails.
* (448) Warning has been added when all the genomes are filtered out and not classified.

Bug Fixes:

* (420 ) Fixed an issue where GTDB-Tk might hang when classifying TIGRFAM markers (`identify`, `classify_wf`, `de_novo_wf`). Special thanks to lfenske-93 and sjaenick for their contribution.
* (428) Fixed an issue where the `--gtdbtk_classification_file` would raise an error trying to read the `classify` summary (`root`, `de_novo_wf`).
* (439) Fix the pipeline when using protein files instead of nucleotide files. symlink uses absolute path instead.

- (399) Fix `--genes` options
- (400) Modify `config.py` file to resolve this issue
- Updated documentation ( including 410 , documentation for itol)