Pore-c-py

Fixed
- model.py: handle case where read is 1-base long and has '*' as quak
Changed
- refactor model.py

Added
- aligns.py: Further annotation of alignments
- aligns.py: extract pairwise alignments
- aligns.py: sort alignments by concatemer_index
- cli.py: add cli tool to generate test data
- align.py: group algnments by concatemer id
- porec: refactor to use generators to avoid memory issues
- utils.py: code to handle sam flags
- io.py: write aligments to sorted bam
- log.py: remove loguru dependency add remora-inspired logging setup
- map.py: find fragment overlaps for alignments
- map.py: add data structure to hold alignments for a concatemer
- index.py: move indexing code to separate file
- test_digest: initial implementation of virtual digest
- Initial-commit: iniital commit
Fixed
- monomers.py: fix edge case for empty cuts
- pyproject.toml: fix broken toml
Changed
- pyproject.toml: remove testw command, can't get it to work
- model.py: move some method logic to functions
- map.py: add multithreaded alignment
- cli.py: update mapping cli
- map.py: move test code into place
- digest.py: use filecollection to manage multiple output
- digest.py: refactor to support mapping
- digest.py: dataclass and pandera schema for digest
- digest.py: move functions out of test code
- pyscaffold: remove old pyscaffold files

Changed
- If `--hi_c` parameter set to true the pairs file will be created.

Changed
- GitHub issue templates
- Nextflow minimum version 23.04.2.
- `--sample_id` parameter has been changed to `--sample` for consistency.
- `--summary_json` optional parameter with default set to true, to include an annotation summary json in outputs.
- Remove `--params_sheet` parameter and add all per sample parameters to sample_sheet.

Added
- `--hi_c` optional parameter with default set to false, to include a `.hic` output file which is compatible with [Juice box](https://www.aidenlab.org/juicebox/).

* Improve schema parameter explanations and output file descriptions in the README.
* Add a default `--chunk_size` parameter value of 25000.
* Update fastcat which removes need to index ubam.
* Enum choices are enumerated in the `--help` output.
* Enum choices are enumerated as part of the error message when a user has selected an invalid choice.
* Bumped minimum required Nextflow version to 22.10.8.

Fixed
- Replaced `--threads` option in fastqingress with hardcoded values to remove warning about undefined `param.threads`

Fixed
- Testing for the cooler tool.