Hybracter

* Replacement of POLCA by [pypolca](https://github.com/gbouras13/pypolca) as it will be easier to integrate, install and maintain going forward, and allows for POLCA use on MacOS.
* Adds `--no_medaka` to skip long read polishing with Medaka.
* Adds per contig stats output tsv file.
* Adds `--dnaapler_custom_db`.
* simone-pignotti fixed some errors with fastp redirection and threads.
* Adds various small improvements (mem for PBS use, various other params and paths, some of the conda envs).

* Fixes [bugs](https://github.com/gbouras13/hybracter/issues/13) with bwa index creation and typos in some output files.
* Thanks simone-pignotti for detecting and fixing [it](https://github.com/gbouras13/hybracter/pull/14)

* Fixes a small [bug](https://github.com/gbouras13/hybracter/issues/9) with samples.smk
* Thanks npbhavya and simone-pignotti for detecting it.

* Initial release.


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Usage: hybracter [OPTIONS] COMMAND [ARGS]...

For more options, run: hybracter command --help

Options:
-h, --help Show this message and exit.

Commands:
install Downloads and installs the plassembler database
hybrid Run hybracter with hybrid long and paired end short reads
hybrid-single Run hybracter hybrid on 1 isolate
long Run hybracter with only long reads
long-single Run hybracter long on 1 isolate
test-hybrid Test hybracter hybrid
test-long Test hybracter long
config Copy the system default config file
citation Print the citation(s) for hybracter
version Print the version for hybracter