.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/archive/
data/*fasta*
data/*metadata*
data/*METADATA*
data/*gisaid*
data/epi
data/zip_codes
data/archives
defaults/colors.tsv
defaults/colors_*.tsv
stats.json

# 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
*~

narratives/*pdf

# zip archives
*.zip

# 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
scripts/data_manipulation/gisaid_meta_to_nextstrain/*.tsv
scripts/data_manipulation/gisaid_meta_to_nextstrain/*.fasta

# specific build files and auxiliary qol files
*B.1.525*
data/sequence_lists/B.1.617_base.txt
data/sequence_lists/B.1.617_belgian.txt
data/sequence_lists/B.1.617_nonbelgian.txttmp.*
*tmp.*
auspice/sars-cov-2-belgium_B.1.617.1*
auspice/sars-cov-2-belgium_B.1.617.2*
auspice/sars-cov-2-belgium_delta*
scripts/data_manipulation/gisaid_meta_to_nextstrain/*.xlsx

*.#*
auspice/*AY.4.2*
data/sequence_lists/rwanda*
auspice/sars-cov-2-belgium_B.1.214*
auspice/sars-cov-2-belgium_eta_small*
.ipynb_checkpoints/
data/test/