Binchicken

* Add extra list and dir arguments
* Update default appraise sequence identity to match SingleM genus-level
* Functional refactoring of scripts

**Full Changelog**: https://github.com/AroneyS/cockatoo/compare/v0.4.4...v0.4.5

* Add initial graph state to clustering search (prevents first edge removal from disconnecting a sample from its largest recover umbrella)
* Supplement recover samples with next best samples (uses relevant unique targets to rank samples)

**Full Changelog**: https://github.com/AroneyS/cockatoo/compare/v0.4.3...v0.4.4

* Changed single assembly recover samples determination. Now uses top N samples ordered by weight. Using graph structure as before produced many samples with only itself as recovery (due to branching from main group before group was smaller than N).

**Full Changelog**: https://github.com/AroneyS/cockatoo/compare/v0.4.2...v0.4.3

* Add SingleM default metapackage support to evaluate
* Add --sample-singlem-list argument
* Switch to symlinking inputs rather than copying

**Full Changelog**: https://github.com/AroneyS/cockatoo/compare/v0.4.1...v0.4.2

* Remove intermediate CoverM files when done
* Update SingleM environment to latest version (Python 3.9, default metapackage via zenodo)
* Add support for metapackage via SINGLEM_METAPACKAGE_PATH environment variable (see SingleM data)


**Full Changelog**: https://github.com/AroneyS/cockatoo/compare/v0.4.0...v0.4.1

Combined cluster and coassemble subcommands as "cockatoo coassemble".

**Full Changelog**: https://github.com/AroneyS/cockatoo/compare/v0.3.0...v0.4.0