.gitignore

# Files created by the pipeline, which we want to keep out of git
# (or at least out of _this_ git repo).

# Downloaded remote files from sources we expect
/nextstrain-ncov-private/
/nextstrain-data/
/data.nextstrain.org/

# Sensitive environment variables
environment*

# Snakemake state dir

# Local config overrides

# For Python #
##############
*.pyc
.tox/
.cache/

# Compiled source #
###################
*.com
*.class
*.dll
*.exe
*.o
*.so

# OS generated files #
######################
.DS_Store
.DS_Store?
._*
.Spotlight-V100
.Trashes
Icon?
ehthumbs.db
Thumbs.db
*~

narratives/*pdf


# metadata / new seqs scripts
scripts/developer_scripts/inputs_new_sequences/
scripts/developer_scripts/output_files_parse_metadata/
scripts/developer_scripts/outputs_new_sequences/

# SLURM log files
slurm-*.out
.snakemake/
.ipynb_checkpoints/
.github/
example-data_frequencies.ipynb
setup.md