Hybracter

* Enforce spades>=v3.15.2 in the `plassembler.yaml` environment
* For some reason, the environment on Linux environments was being solved for v3.14.1, which was causing an error with Unicycler within Plassembler for some samples described (https://github.com/rrwick/Unicycler/issues/318)

* Adds 'circualr=True' to chromosome contig headers where Flye has marked these as such. This bug was introduced in v0.7.0.
* Thanks Nicole Lerminiaux for spotting this

* Fixes bug where `hybracter install -d db_dir` would not work as the `-f` parameter was not being passed to Plassembler. Thanks npbhavya

**Bug fixes**

* Fixes bug where `--configfile` wasn't being passed to Hybracter.
* Fixes bug where `hybracter` would crash if the input long reads were not gzipped 51 thanks wanyuac.

**Changes to short read polishing.**

* Logic added to run `polypolish` v0.6.0 with `--careful` and skip pypolca if the SR coverage estimate is below 5x (note: FASTA files for pypolca will be generated in the processing directory to play nice with Snakemake, but these will be identical to the polypolish output).
* For 5-25x coverage, `polypolish --careful` and `pypolca` with `--careful` will be run.
* For >25x coverage, `polypolish` default and `pypolca` with `--careful` will be run.
* A preprint justifying these changes will be available soon.

**`--logic` changes**
* By default, `--logic` defaults to `last` for `hybracter hybrid`, as there we have found that the polishing strategy implemented above never makes the assembly worse. We suggest never using `--logic best` with `hybracter hybrid`.

**Changes for chromosome contigs and circularity.**
* If hybracter assembles a contig that is greater than the minimum chromosome length but not marked as circular by Flye, this will now be denoted as a chromosome, but not circular. The genome will be marked as complete also.
* These will usually be assemblies with some issue (e.g. prophages, circularisation issues, heterogeneity) and probably require some more attention.
* For example, with the _Vibrio cholerae_ larger chromosome described [here](https://rrwick.github.io/2024/02/15/misassemblies.html), the genome will be marked as 'complete' but the contig will not be marked as 'circular' in the `hybracter` output.
* Such contigs will be polished and be in the final `_chromosome.fasta` output, but they will not be rotated by `dnaapler`.
* These were previously being excluded, which was missing assemblies with structural heterogeneity (causing the chromosome not to completely circularise) or even bacteria with linear chromosomes like [_Borrelia_](https://www.nature.com/articles/37551).

**Adds `--depth_filter`**
* This is passed to [Plassembler](https://github.com/gbouras13/plassembler) and will filter out all putative plasmid contigs that are lower than this depth fraction compared to the chromosome.
* Defaults to 0.25 like Unicycler's implementation.

* 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.