# Local study configuration and data
/config.local.json
*.local.json
*.local.config
/ui_configs/
/inputs/
/data/
*.d/
*.raw
*.RAW
*.mzML
*.mzXML
*.wiff
*.wiff2
*.tdf
*.tdf_bin
*.fasta
*.fa
*.fastq*
# Generated results, caches, and installed modules
/results*/
/final_results*/
/analysis_details/
/work*/
/logs/
/.nextflow*
/.runtime/
/.test-runtime*/
/.bootstrap/
/.database_cache/
/modules/*
!/modules/diapasef/
/provenance/
/reference_results/
__pycache__/
*.pyc
.venv*/
# Registered software, archives and credentials
/software/
*.jar
*.zip
*.tar.gz
.env
.env.*
*registration*
*license_key*
*.pem
*.key

/zscore/
/VALIDATION_COMPLETE.txt

# Local caches, backups, preparation and study artifacts
/cache/
/configs/
/.migration_backup/
/.ipynb_checkpoints/
*.ipynb
*.log
*.log.*
*.pid
*.parquet
*.speclib
*.mzBIN*
*.quant

# Imported provider tables and review artifacts stay local
/service_quantification/
/imports/
/benchmarks/
/validation/
/*.csv
/*.tsv
/*.xlsx

# Python distributions and launcher state
/build/
/dist/
*.egg-info/
.fun_proteomics/
/src/fun_proteomics/_workflow/
