Hybracter

* Fixes bug with Polypolish v0.6.0 breaking the CLI 48
* Adds `-m` option to download all Medaka models with `hybracter install` - useful for offline use 49
* Adds quick SR coverage estimates (in `processing/qc/coverage`) and other QC stats (using [seqkit](https://bioinf.shenwei.me/seqkit/) ) in `processing/qc/seqkit`. This is calculated as (Total bases / estimated chromosome size) for each sample
* Logic added to run Polypolish and pypolca with `--careful` if the SR coverage estimate is below 25x.

Ryan Wick recently ran `hybracter long` on the latest Dorado v0.5.0 Nanopore reads (his [blog post](https://rrwick.github.io/2023/12/18/ont-only-accuracy-update.html)). You can read a write-up of the results [here](https://hybracter.readthedocs.io/en/latest/dorado_ryan_louise_0_5_0/).

* Adds subsampling using `--subsample_depth` using Filtlong, based on some benchmarking of Dorado v0.5.0. Defaults to 100x of the estimated chromosome size `-c`.
* Adds stricter criteria for complete assemblies (aka ensures that identified chromosomes must be circularised according to Flye). Thanks to Matthew Croxen for pointing this out.

* Updates code to work with updated version of Plassembler v1.5.0
* Thanks [npbhavya](https://github.com/npbhavya) for finding this.

* Adds `--logic` parameter. You have 2 choices: `--logic best` (the default) or `--logic last`.
* `--logic best` will run `hybracter` as normal and the best assembly (by ALE or pyrodigal mean length) will be selected as the final assembly.
* `--logic last` will force hybracter to pick the last polished round as the final assembly even if it is not the best as per ALE/pyrodigal. So for `hybracter hybrid` this will default to the pypolca polished round. You may wish to use this if you want all your isolates to be consistently assembled.
* Adds reorientation of pre polished chromosome in case it is selected as the best assembly
* Adds fixes to the chromosome comparisons - now it is much easier to interpret any changes between conditions.

* Fixes bug relating to polishing. Prior to v0.3.0, hybracter would only polish the chromosome with the entire readset. Benchmarking revealed that if there was significantly similarity between chromosome and plasmids, polishing would introduce errors. Now the entire assembly (chromosome from Flye + plasmids from Plassembler) is polished in every polishing step with improved results. Upgrading and re-running hybracter is recommended.
* Fixes small bugs in output .tsvs.

* Fixes small bugs relating to isolates with multiple chromosomes like ATCC17802
* Add temp files for intermediate FASTQ files and cleans up BAM, SAM and hdf files from Medaka and polypolish to reduce output size