.gitignore

# Files created by the pipeline, which we want to keep out of git
# (or at least out of _this_ git repo).
benchmarks/
logs/
results/
build/
auspice/
data/*
defaults/colors.tsv
defaults/colors_*.tsv
stats.json

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

# Sensitive environment variables
environment*

# Snakemake state dir
/.snakemake
snakemake_log

# Local config overrides
/config_local.yaml

# 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
*~

# IDE generated files #
######################
.vscode/

narratives/*pdf


# metadata / new seqs scripts
scripts/curate_metadata/inputs_new_sequences/
scripts/curate_metadata/output_curate_metadata/
scripts/curate_metadata/outputs_new_sequences/
scripts/curate_metadata/config_curate_metadata/geoLocationRules.txt
scripts/curate_metadata/config_curate_metadata/manualAnnotationRules.txt


# SLURM log files
slurm-*.out