.gitignore

### Nextflow-Libs ###
/feature_gen_test/FEATURE-GEN/Archive_NFParser

### Bioinformatics ###
*.fasta
*.fastq
*.tar
*.gz
*.fa
*.fq
*.fasta.gz
*.fastq.gz
*.fa.gz
*.fq.gz
token.txt
!test_data_1.fq.gz
!test_data_2.fq.gz
*.sif
/bacerial_isolates
/unused
/feature_gen_lib/tmp

### Emacs ###
# -*- mode: gitignore; -*-
*~
\#*\#
/.emacs.desktop
/.emacs.desktop.lock
*.elc
auto-save-list
tramp
.\#*

# Org-mode
.org-id-locations
*_archive

# flymake-mode
*_flymake.*

# eshell files
/eshell/history
/eshell/lastdir

# elpa packages
/elpa/

# reftex files
*.rel

# AUCTeX auto folder
/auto/

# cask packages
.cask/
dist/

# Flycheck
flycheck_*.el

# server auth directory
/server/

# projectiles files
.projectile

# directory configuration
.dir-locals.el

# network security
/network-security.data


### Groovy ###
# .gitignore created from Groovy contributors in https://github.com/apache/groovy/blob/master/.gitignore

user.gradle
.gradle/
target/
build/
out/

*.DS_Store
*.class
*.swp

.idea
*.iml
*.ipr
*.iws
.shelf

.settings/
.classpath
.project

### Linux ###

# temporary files which can be created if a process still has a handle open of a deleted file
.fuse_hidden*

# KDE directory preferences
.directory

# Linux trash folder which might appear on any partition or disk
.Trash-*

# .nfs files are created when an open file is removed but is still being accessed
.nfs*

### macOS ###
# General
.DS_Store
.AppleDouble
.LSOverride

# Icon must end with two \r
Icon

# Thumbnails
._*

# Files that might appear in the root of a volume
.DocumentRevisions-V100
.fseventsd
.Spotlight-V100
.TemporaryItems
.Trashes
.VolumeIcon.icns
.com.apple.timemachine.donotpresent

# Directories potentially created on remote AFP share
.AppleDB
.AppleDesktop
Network Trash Folder
Temporary Items
.apdisk

### macOS Patch ###
# iCloud generated files
*.icloud

### Nanoc ###
# For projects using Nanoc (http://nanoc.ws/)

# Default location for output (needs to match output_dir's value found in nanoc.yaml)
output/

# Temporary file directory
tmp/nanoc/

# Crash Log
crash.log

### PowerShell ###
# Exclude packaged modules
*.zip

# Exclude .NET assemblies from source
*.dll

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

# C extensions
*.so

# 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/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/
.pytest_cache/
cover/

# 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
.pybuilder/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py
.pdm.toml

# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
__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/

# pytype static type analyzer
.pytype/

# Cython debug symbols
cython_debug/

### Python Patch ###
# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
poetry.toml

# ruff
.ruff_cache/

# LSP config files
pyrightconfig.json

### Vim ###
# Swap
[._]*.s[a-v][a-z]
!*.svg  # comment out if you don't need vector files
[._]*.sw[a-p]
[._]s[a-rt-v][a-z]
[._]ss[a-gi-z]
[._]sw[a-p]

# Session
Session.vim
Sessionx.vim

# Temporary
.netrwhist
# Auto-generated tag files
tags
# Persistent undo
[._]*.un~

### Windows ###
# Windows thumbnail cache files
Thumbs.db
Thumbs.db:encryptable
ehthumbs.db
ehthumbs_vista.db

# Dump file
*.stackdump

# Folder config file
[Dd]esktop.ini

# Recycle Bin used on file shares
$RECYCLE.BIN/

# Windows Installer files
*.cab
*.msi
*.msix
*.msm
*.msp

# Windows shortcuts
*.lnk