.gitignore

# text files
*.error
*.gff
*.gtf
*.fa
*.txt
*.toml

# large file formats
*.gz
*.bam
.DS_Store
.vscode
#nextflow related files
.nextflow*
work
data/*/

# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
pip-wheel-metadata/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# 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
!*app1.manifest
!*app.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/
.pytest_cache/

# Translations
*.mo
*.pot

# Django stuff:
*.log
local_settings.py
db.sqlite3
db.sqlite3-journal

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# PyBuilder
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
.python-version

# pipenv
#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
#   However, in case of collaboration, if having platform-specific dependencies or dependencies
#   having no cross-platform support, pipenv may install dependencies that don't work, or not
#   install all needed dependencies.
#Pipfile.lock

# PEP 582; used by e.g. github.com/David-OConnor/pyflow
__pypackages__/

# Celery stuff
celerybeat-schedule
celerybeat.pid

# SageMath parsed files
*.sage.py

# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# Pyre type checker
.pyre/

## Ignore Visual Studio temporary files, build results, and
## files generated by popular Visual Studio add-ons.

# User-specific files
*.suo
*.user
*.userosscache
*.sln.docstates

# User-specific files (MonoDevelop/Xamarin Studio)
*.userprefs

# Build results
[Dd]ebug/
[Dd]ebugPublic/
[Rr]elease/
[Rr]eleases/
x64/
x86/
bld/
[Bb]in/
[Oo]bj/

# Visual Studio 2015 cache/options directory
.vs/
# Uncomment if you have tasks that create the project's static files in wwwroot
#wwwroot/

# MSTest test Results
[Tt]est[Rr]esult*/
[Bb]uild[Ll]og.*

# NUNIT
*.VisualState.xml
TestResult.xml

# Build Results of an ATL Project
[Dd]ebugPS/
[Rr]eleasePS/
dlldata.c

# DNX
project.lock.json
artifacts/

*_i.c
*_p.c
*_i.h
*.ilk
*.meta
*.obj
*.pch
*.pdb
*.pgc
*.pgd
*.rsp
*.sbr
*.tlb
*.tli
*.tlh
*.tmp
*.tmp_proj
*.log
*.vspscc
*.vssscc
.builds
*.pidb
*.svclog
*.scc

# Chutzpah Test files
_Chutzpah*

# Visual C++ cache files
ipch/
*.aps
*.ncb
*.opendb
*.opensdf
*.sdf
*.cachefile

# Visual Studio profiler
*.psess
*.vsp
*.vspx
*.sap

# TFS 2012 Local Workspace
$tf/

# Guidance Automation Toolkit
*.gpState

# ReSharper is a .NET coding add-in
_ReSharper*/
*.[Rr]e[Ss]harper
*.DotSettings.user

# JustCode is a .NET coding add-in
.JustCode

# TeamCity is a build add-in
_TeamCity*

# DotCover is a Code Coverage Tool
*.dotCover

# NCrunch
_NCrunch_*
.*crunch*.local.xml
nCrunchTemp_*

# MightyMoose
*.mm.*
AutoTest.Net/

# Web workbench (sass)
.sass-cache/

# Installshield output folder
[Ee]xpress/

# DocProject is a documentation generator add-in
DocProject/buildhelp/
DocProject/Help/*.HxT
DocProject/Help/*.HxC
DocProject/Help/*.hhc
DocProject/Help/*.hhk
DocProject/Help/*.hhp
DocProject/Help/Html2
DocProject/Help/html

# Click-Once directory
publish/

# Publish Web Output
*.[Pp]ublish.xml
*.azurePubxml
# TODO: Comment the next line if you want to checkin your web deploy settings 
# but database connection strings (with potential passwords) will be unencrypted
*.pubxml
*.publishproj

# NuGet Packages
*.nupkg
# The packages folder can be ignored because of Package Restore
**/packages/*
# except build/, which is used as an MSBuild target.
!**/packages/build/
# Uncomment if necessary however generally it will be regenerated when needed
#!**/packages/repositories.config

# Microsoft Azure Build Output
csx/
*.build.csdef

# Microsoft Azure Emulator
ecf/
rcf/

# Microsoft Azure ApplicationInsights config file
ApplicationInsights.config

# Windows Store app package directory
AppPackages/
BundleArtifacts/

# Visual Studio cache files
# files ending in .cache can be ignored
*.[Cc]ache
# but keep track of directories ending in .cache
!*.[Cc]ache/

# Others
ClientBin/
~$*
*~
*.dbmdl
*.dbproj.schemaview
*.pfx
*.publishsettings
node_modules/
orleans.codegen.cs

# RIA/Silverlight projects
Generated_Code/

# Backup & report files from converting an old project file
# to a newer Visual Studio version. Backup files are not needed,
# because we have git ;-)
_UpgradeReport_Files/
Backup*/
UpgradeLog*.XML
UpgradeLog*.htm

# SQL Server files
*.mdf
*.ldf

# Business Intelligence projects
*.rdl.data
*.bim.layout
*.bim_*.settings

# Microsoft Fakes
FakesAssemblies/

# GhostDoc plugin setting file
*.GhostDoc.xml

# Node.js Tools for Visual Studio
.ntvs_analysis.dat

# Visual Studio 6 build log
*.plg

# Visual Studio 6 workspace options file
*.opt

# Visual Studio LightSwitch build output
**/*.HTMLClient/GeneratedArtifacts
**/*.DesktopClient/GeneratedArtifacts
**/*.DesktopClient/ModelManifest.xml
**/*.Server/GeneratedArtifacts
**/*.Server/ModelManifest.xml
_Pvt_Extensions

# Paket dependency manager
.paket/paket.exe

# FAKE - F# Make
.fake/

# local data files
output
results
# ignore large output files saved to local
*fasta
*tsv
*xlsx