.gitignore

# Files created by the pipeline, which we want to keep out of git
data/
logs/
results/
benchmarks/
sequence-counts/
mlr-estimates/

# Specific Auspice JSONs
ncov_gisaid_global_all-time.json
ncov_gisaid_global_all-time_root-sequence.json
ncov_gisaid_global_all-time_tip-frequencies.json
nextclade_sars-cov-2.json
nextclade_sars-cov-2_flat.json
nextclade_sars-cov-2_root-sequence.json

# Specific ESM files
embeddings_pretrained.tsv
embeddings_fine_tuned.tsv

# Compiled manuscript files
fitness_flux.pdf

# Errors from tests
*.err

# From Snakemake
.snakemake/

# Sensitive environment variables
environment*

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

# LaTeX intermediaries #
########################
*.aux
*.log
*.bbl
*.blg
*.out

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

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