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.gitignore
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# Folders
.vscode
.snakemake
Hotpep/
output/
prokka/
reports/
report/*
results/*
notebook/
logs/
data/
drafts/
.tests
AfterFS
example_data_results
old_data/
tmp/*
dag.pdf
example_data/SRR9067257*
benchmarks
testing
results_security
config/config.yaml
#Ignore databases folder, except some specific files:
databases/*
!databases/lib/*
!databases/config-template.yml
!databases/exec_annotation
!databases/merops_ids.csv
!databases/Pfam-A.clans.tsv
!databases/cdd2cog.pl
!databases/cdd2cog2.pl
!databases/cog_mappings.tsv
!databases/pdb_pfam_mapping.txt
!databases/idmapping_KO.tab.gz
!databases/ko_mappings.tsv
!databases/Feature_selection.csv
workflow/databases/*
!workflow/databases/lib/*
!workflow/databases/config-template.yml
!workflow/databases/exec_annotation
!workflow/databases/merops_ids.csv
!workflow/databases/Pfam-A.clans.tsv
!workflow/databases/cdd2cog.pl
!workflow/databases/cdd2cog2.pl
!workflow/databases/cog_mappings.tsv
!workflow/databases/pdb_pfam_mapping.txt
!workflow/databases/idmapping_KO.tab.gz
!workflow/databases/ko_mappings.tsv
!workflow/databases/Feature_selection.csv
#Files
example_data/Aq78_pacbio.fa
example_data/Aq107_pacbio.fa
example_data/Aq135_pacbio.fa
example_data/Aq349_pacbio.fa
example_data/EL43_pacbio.fa
temp*
workspace.code-workspace
drafts
report.html
dag.svg
Aq_sp_Aq107.fna
# 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
*.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/
#R
.Rhistory
.RData
.~lock*
5_Melange_test/OG0000001.fa
example_data/OG0000001.fa