pangenoma/.gitignore at develop · vogonverse/pangenoma · GitHub

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# .gitignore - Pipeline PanForest
# ===============================

# ============================================
# SNAKEMAKE - Outputs and temporary files
# ============================================
.snakemake/
logs/
benchmarks/
*.log
slurm-*.out

# ============================================
# RESULTS - Generated files
# ============================================
results/
data/interim/*
data/final/*

# Random Forest batch processing
data/interim/rf_batches/
results/random_forest/batches/

# D Statistic batch processing
data/interim/d_stat_batches/
results/statistics/batches/

# Keep directory structure
!results/.gitkeep
!data/interim/.gitkeep
!data/final/.gitkeep

# ============================================
# RAW DATA - Downloaded genomes
# ============================================
data/raw/genomes/genomes/
data/raw/genomes/ncbi_metadata.jsonl
data/raw/genomes/gff_files.txt
data/raw/genomes/accessions_filtered.txt
data/raw/genomes/deduplication_stats.txt
data/raw/ncbi_dataset/
data/raw/*.gff
data/raw/*.gbk
data/raw/*.fna
data/raw/*.faa
data/raw/*.fasta
data/raw/*.fa
data/raw/*.fastq
data/raw/*.fastq.gz

# Keep original repo data for Panaroo output from paper (gene_presence_absence.csv)
!data/raw/example_*.csv
!data/raw/.gitkeep

# ============================================
# PANAROO - Large intermediate outputs
# ============================================
# If Panaroo generates outputs in data/raw, ignore them
data/raw/panaroo_output/
data/raw/gene_data/
data/raw/*.aln
data/raw/*.tree
data/raw/*.nwk
data/raw/*.phy

# ============================================
# PYTHON - Bytecode and cache
# ============================================
__pycache__/
*.py[cod]
*$py.class
*.so
.Python
*.egg
*.egg-info/
dist/
build/
.eggs/
pip-log.txt
pip-delete-this-directory.txt


# ============================================
# R - Temporary files and data
# ============================================
.Rhistory
.RData
.Rproj.user
*.Rproj
.Rapp.history
*_cache/
/cache/

# ============================================
# CONDA
# ============================================
.conda/
*.tar.bz2
.snakemake/conda/
workflow/envs/.conda/

# ============================================
# REGENERABLE GRAPHICS
# ============================================
dag.png
rulegraph.png
filegraph.png
*.pdf
*.svg

# Keep final figures
!results/figures/paper_*.png
!results/figures/paper_*.pdf

# ============================================
# DATABASE
# ============================================
results/database/*.db
results/database/*.sqlite
results/database/*.sqlite3
*.db-journal

# ============================================
# LARGE CSV - Importance matrices
# ============================================
# results/random_forest/imp.csv
# results/networks/simplified_imp.csv

# ============================================
# IDEs
# ============================================
# VSCode
.vscode/
*.code-workspace

# ============================================
# OPERATING SYSTEM
# ============================================
# Linux
.directory
.Trash-*

# ============================================
# DOCUMENTATION
# ============================================
CLUSTER_USAGE.md