Hybracter

* Changes Medaka env to use pip - see this issue https://github.com/nanoporetech/medaka/issues/547 - thanks William Shropshire for investigating and alerting me to this and Matthew Croxen for noticing in the first place
* Using pip is 5-10x faster

* Bug fix for `--contaminants` that was profoundly broken (https://github.com/gbouras13/hybracter/issues/115) thanks nbat64
* Bug fix to support for dnaapler v1.1.0 with `--db "dnaa,cog1474,repa"` (https://github.com/gbouras13/hybracter/issues/116)

* Replaces [kmc](https://github.com/refresh-bio/KMC) with [lrge](https://github.com/mbhall88/lrge) when using `--auto`, a much faster tool designed for the purpose of estimating genome size from long reads. It is very very fast and robust.
* If you input has more than 5000 long reads (it should!), [lrge](https://github.com/mbhall88/lrge) will run in default settings. If it has under this, then it will run a (slightly) more computationally expensive all-vs-all mode with all input reads. In practice, if you have such low read counts, you should take all downstream analysis (inclduing lrge and hybracter) with a lot of caution anyway.
* According to the [preprint](https://www.biorxiv.org/content/10.1101/2024.11.27.625777v1) (and my less exhaustive testing), lrge is more accurate and much faster than kmc, but I would still be careful using it on data that has lower quality than < Q15.
* Nothing else changes - the estimated chromosome size used by Hybracter will still be 80% of the estimate, as it needs to account for plasmids
* Adds `r1041_e82_400bps_bacterial_methylation` as an option for `--medakaModel` thanks to [this issue](https://github.com/gbouras13/hybracter/issues/108).
* Note this won't work if you run `hybracter` on a Mac (as medaka v2 is not available)

* Adds retry functionality for dnaapler with 1 thread if there is an error - for some genomes on some systems, [it was observed](https://github.com/gbouras13/hybracter/issues/54) that using the default resources (8 threads, 16GB RAM) will lead to an error in dnaapler.
* Thanks [richardstoeckl](https://github.com/richardstoeckl) for implementing this
* Thanks to some feedback from [oschwengers](https://github.com/oschwengers), modify documentation to warn users that for low quality long read sets (e.g. R9 FAST/HAC or sub Q15 reads), `--auto` is _not_ recommended. It can tend to overestimate the chromosome size as more erroneous 21-mers will be counted by kmc than expected. Please specify a chromosome size for this type of data going forward.

* Updates Medaka to v2.0.1, implementing the `--bacteria` option by default.
* This is based on the recommendations of Ryan Wick [here](https://rrwick.github.io/2024/10/17/medaka-v2.html) who found it improved assemblies due to (likely) enhanced methylation error correction.
* If you still want to specify a Medaka model, the flag `--medaka_override` has been added. You need to include this along with your model via `--medakaModel`. This is most likely useful for older R9 data.
* Adds `--extra_params_flye` parameter if you want to specify extra commands for the Flye assembly step thanks pdobbler.

* Small change to the `plassembler.yaml` config preventing installation bugs - Unicycler v0.5.1 to be installed in a much simpler fashion via Bioconda