V0.5

.gitignore

@@ -1,170 +1,8 @@
-#dev
-# NOTE: For .gitignore, order matters. The last match wins. meaning if you want to ignore a folder but keep something in the folder, first ignore the folder, then unignore the file.
-.venv
-
-token
-# input/output is designed as a generic folder for input files if the config isn't adjusted. Because of this we want to ensure it's documented out. As it'll be an empty folder a .gitkeep file is used for git to maintain the structure.
-input/*
-!input/.gitkeep
-output/*
-!output/.gitkeep
-# The config folder is intended to keep multiple program configs, these are sensitive to the system, a default is included for people to work off of while the others are hidden
-#config/*
-# If you are using pypi integration
-.pypirc
-
-examples/
+.snakemake/
+Logs
+__pycache__**
+examples/Results/
+examples/results/
+examples/Dataset/reads/*gz
 resources/
-output/
-
-_proc/
-# The following files ignored are part of a standard python project with minor additions
-_docs/
-
-*.bak
-.gitattributes
-.last_checked
-.gitconfig
-*.bak
-*.log
-*~
-~*
-_tmp*
-tmp*
-tags
-*.pkg
-
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-env/
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-.hypothesis/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# pyenv
-.python-version
-
-# celery beat schedule file
-celerybeat-schedule
-
-# SageMath parsed files
-*.sage.py
-
-# dotenv
-.env
-
-# virtualenv
-.venv
-venv/
-ENV/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-
-*.swp
-
-# osx generated files
-.DS_Store
-.DS_Store?
-.Trashes
-ehthumbs.db
-Thumbs.db
-.idea
-
-# pytest
-.pytest_cache
-
-# tools/trust-doc-nbs
-docs_src/.last_checked
-
-# symlinks to fastai
-docs_src/fastai
-tools/fastai
-
-# link checker
-checklink/cookies.txt
-
-# .gitconfig is now autogenerated
-.gitconfig
-
-# Quarto installer
-.deb
-.pkg
 
-# Quarto
-.quarto