.gitignore

# 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/

# vm
clockwork

# snakemake
.snakemake

# reference genome index
reference_genome.fasta.amb
reference_genome.fasta.ann
reference_genome.fasta.bwt
reference_genome.fasta.fai
reference_genome.fasta.pac
reference_genome.fasta.sa

# software
nextflow

# outputs
phastSim_output
simulated_genomes
tree_populations.txt
amplicon_sequences
updated_sequences
ART_read_output
Badread_read_output
concatenated_ART_reads
concatenated_Badread_reads
viridian_ART_assemblies
viridian_Badread_assemblies
epi2me_Badread_assemblies
masked_truth_assemblies
truth_vcfs
varifier_statistics
phylogeny_comparisons
cte_output
artic_ART_assemblies
usher_phylogenies
changed_nodes
final-tree.nh
mutation-paths.txt
placement_stats.tsv
artic_vcfs
cte_artic_output
cte_viridian_output
logs

# singularity containers
singularity/images
singularity/usher
singularity/varifier
singularity/viridian_workflow
singularity/covid-truth-eval
singularity/ushonium
singularity/ncov2019-artic-nf
singularity/epi2me