Sphae

- db_dir variable error fixed
- moving to using mamba instead of conda as default
- updating setup.py to pyproject.toml

- checkv database error fixed
- updating phold.yaml and medaka.yaml file
- updated to set the databases to variables that need to be set by the user
- this to so the users download only those databases they dont have
- `sphae install` still works to install all the required databases, but the variables still have to be set to run `sphae run`
- example of how to set these variables are set in `sphae.sh`

- updating sphae code to make it a smaller container
- fixing rules to allow --conda-create-envs-only
- adding a phylogeny module to sphae annotate

- catches a specific cases of having mutiple circular phages from assembly
- updating the code to count number of hypothetical proteins to catch other genes that dont have a biological function assigned
- Addressing issue36- Phrogs annotated toxin not recognised in sphae summary output

- adding the option to run pharokka with --pyrodigal-gv to test for alternate coding genes in config file
- sphae plots fix

- Summary file update
- missed adding DTR found or not when only one genome assembled per sample, added this in now
- If recombinases or transposases are found, the genes are written to the summary. Also if AMR, virulence genes, CRSIPR spacers etc are found.
The files are written output.
- Updating the QC rule to touch the output file so the error is correctly recorded
- the annotate function table after the 3Ps werent being generated, so added that in
- add the number of unknown proteins to the final summary file
- updated phynteny yaml file to include numpy version
- added a python script to the misc folder to merge the RESULTS to one tsv file
- adding the total read length to summary file
- updating the taxa description in the summary file to include the taxa description, lowest taxa and the isolated host from the pharokka inphared result
- added the --no-polish option