zenodo_10086238/ 

# CWL temporary files
*.tmp
*_tmp/
cwl_tmp*/

# Output files
final_reports/
finalHaplotypList_*.csv
finalSNPList_*.csv
analysis_summary.json
HaplotypeList_*.fasta

# Intermediate analysis files
*_mutations_detailed_analysis.csv*
*_mutations_resistance_summary.csv*
*_dada2_haplotypes.fasta*
*_filter_stats.txt*
*_counts.csv*

# Python cache
__pycache__/
*.pyc
*.pyo

# R files
*.RData
*.Rhistory

# Investigation and validation files (keep documentation)
# INVESTIGATION_REPORT.md
# VALIDATION_RESULTS.md

# Temporary scripts
create_quality_subset.py

# Large data directories (keep structure but ignore contents)
zenodo_10086238/rawData/
test-data/

# OS files
.DS_Store
Thumbs.db
