Chewbbaca

Added the Sequence Logo component to the individual reports of SchemaEvaluator.

- Bugfix to fix issue when users provided a text file with the paths to the input genome assemblies or genes to use in the CreateSchema or AlleleCall processes.

- Bugfix to fix issue in the PrepExternalSchema process when BLAST >= v2.10 was used.

New implementation of the **UniprotFinder** process. A new feature allows users to specify a set of taxa and determine annotation terms based on matches against UniProt's reference proteomes for those taxa.

New implementation of the **CreateSchema** process. This new implementation significantly reduces execution time. It is designed to enable schema creation based on hundreds or thousands of assemblies on a laptop. The schemas generated by the new implementation are fully compatible with previous versions.

Additional changes

- Improved detection of invalid inputs (inputs that do not contain coding sequences (CDSs), that contain invalid sequences/characters, empty files, etc).
- New parameter `--pm` allows users to set Prodigal's execution mode. The `single` mode is the default mode. Use the `meta` mode for input files that have less than 100kbp (e.g.: plasmids, viruses).
- `CreateSchema` accepts a single or several FASTA files with CDSs if the `--CDS` option is included in the command. This option skips the gene prediction step with Prodigal and creates a schema seed based on the CDSs in the input files.
- `AlleleCall` can automatically detect parameter values previously used with a schema. Users only need to provide values for the `-i`, `-g` and `-o` parameters.

The **SchemaEvaluator** module was refactored due to unsupported dependencies that were not allowing the report generation. The style of the report is similar to the what can be found on [Chewie-NS](https://chewbbaca.online/).

More in-depth information can be found about the module on its [wiki page](https://github.com/B-UMMI/chewBBACA/wiki/4.-Schema-Evaluation).