Somaticseq

Accepts complex variants from VCF files but convert them into snvs and indels.

Bug fix
- Fixed a misplaced `,` that broke the `--help` function in `somaticseq_run_workflows`. The script was still functional but the `--help` message could not print.
- Fixed links in README due to `example` moving to `tests/example`.

Mostly for maintenance
- Add `pyproject.toml` to modernize build scripts for `pip install .` as `./setup.py install` is being deprecated by python.
- Additional entrypoints for scripts shown in `pyproject.toml`. Scripts in `setup.py` are kept to be backward-compatible to previous command line interface.
- Extra packages for development can be installed via `pip install '.[dev]'`.
- Add an initial test in `tests` and moved `example` there.
- Refactored some functions

Mostly maintenance
- A lot of coding stylistic changes to make things more modern and easier to maintain
- Enforce versioning for some dependencies in `setup.py`, including `python>=3.10`
- For XGBoost model, additionally output json file (i.e., decision trees)
- Updated some docker files for 3rd party tools
- remove `-d dbsnp.vcf.gz` parameter from tumor-only LoFreq command (that param is only meaningful for tumor-normal pair)

**Full Changelog**: https://github.com/bioinform/somaticseq/compare/v3.7.4...v3.8.0

ntree_limit is replaced with iteration_range in xgboost.predict in xgboost >=1.4. This release uses `iteration_range=(0, iterations)` instead of `ntree_limit=iterations`.

Allow xgboost hyperparameters be passed into `somaticseq_parallel.py`, e.g., `somaticseq_parallel.py --somaticseq-train --extra-hyperparameters scale_pos_weight:0.1 seed:100`. Previously, they could only be passed into `somatic_xgboost.py`. Beware, however, multi-argument options like `--extra-hyperparameters` and `--features-excluded` cannot be placed immediately before `paired` or `single`, because otherwise it'll try to include `paired` or `single` as an argument instead of invoking `paired` or `single` mode.