Pharokka

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* Fixes bug introduced by Pyhmmer's upgrade to v0.11.0 (https://github.com/gbouras13/pharokka/issues/375).
* Fixes bug where Pyhmmer could not infer the amino acid alphabet by explictly inferring it (https://github.com/gbouras13/pharokka/issues/331) (https://github.com/gbouras13/pharokka/issues/357)
* Fixed one-off start CDS coordinate bug where using `--genbank` (https://github.com/gbouras13/pharokka/issues/353)

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* Adds `--trna_scan_model` parameter with two accepted options: `--trna_scan_model general` (this will be run by default - what Pharokka has always been running) and `--trna_scan_model bacterial`. See the [tRNAscan-SE paper](https://doi.org/10.1093/nar/gkab688) for more information.
* Bumps the `dnaapler` dependency to v1.0.1 due to a breaking dependency change in `dnaapler`.

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* Fixes issue with genbank creation if certain CARD hits are found [issue 339](https://github.com/gbouras13/pharokka/issues/339)).
* Due to some semi-colons in the CARD metadata, new qualifier keys were being made in error.
* Solved by removing semicolons in the updated CARD metadata sheet

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* Identifies issue if `` is input contig header - Pharokka will error if your contig headers contain this character and prompt you to remove them

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* Adds Google Colab notebook that can run pharokka and [phold](https://github.com/gbouras13/phold).
* The notebook is [https://colab.research.google.com/github/gbouras13/pharokka/blob/master/run_pharokka_and_phold.ipynb](https://colab.research.google.com/github/gbouras13/pharokka/blob/master/run_pharokka_and_phold.ipynb)
* Fixes 334 issues with contig ids if they were in scientific notation or lead with 0s.
* Fixes issues with `pharokka_proteins.py` not outputting PHROG annotations.

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* Adds `pharokka_multiplotter.py` to plot multiple phage contigs at once
* Adds separate contig FASTA files if `-s -m` is run (in `single_fastas`)