Stpipeline

* Refactor code to modern Python (black, mypy, isort)
* Added Github Actions
* Added pre-commit hooks
* Changed the build configuration to Poetry
* Added a Docker container
* Changed tests to pytest
* Updated versions of dependencies
* Performed code optimizations, refactorings and clean ups
* Added more tests for almost full coveragge
* Bumped taggd to 0.4.0
* Changed documentation
* Added --demultiplex-chunk-size option

* Added annotation (htseq) feature type as parameter

* Fix a small bug when having the UMI before the BARCODE

* Improved the unit-tests
* Make input data a positional arguments in extra scripts

* --ref-map is not a required parameter now when --disable_mapping is used
* Create dataset and compute saturation steps are only performed if the annotated
file is present
* Fixed bug in merge_fastq.py
* Fixed bugs in st_qa.py

* Updated docs
* Added flags to skip (trimming, mapping and annotation)
* Fixed a bug in the compute saturation option
* Restored the unittests
* Improvements when dealing with ambiguous and no_feature genes