# Python
__pycache__/
*.py[cod]
*.egg-info/
.venv/
.pytest_cache/
.mypy_cache/
.ruff_cache/

# Bioflow runtime
.bioflow_state.json
data/test/**/out/
data/references/dbs/**
data/references/genomes/**
!data/references/.gitkeep
!data/references/dbs/.gitkeep
!data/references/genomes/.gitkeep

# OS
.DS_Store
Thumbs.db

# Comparative genomics analysis outputs (regeneratable)
analysis/*/genomes/
analysis/*/genomes_full/
analysis/*/inputs/
analysis/*/prokka/
analysis/*/roary/
analysis/*/fastani/
analysis/*/fastani_full/ani_full.tsv
analysis/*/scoary/results/
analysis/*/run.log
analysis/*/full_ani.log
analysis/*/download_full.log
analysis/*/fastani_full/genomes.txt
# IQ-TREE intermediate files (keep only the *.treefile)
analysis/*/phylogeny/*.bionj
analysis/*/phylogeny/*.iqtree
analysis/*/phylogeny/*.log
analysis/*/phylogeny/*.mldist
analysis/*/phylogeny/*.splits.nex
analysis/*/phylogeny/*.uniqueseq.phy
analysis/*/phylogeny/*.contree
analysis/*/phylogeny/*.ckp.gz
analysis/*/phylogeny/*.model.gz
analysis/*/prokka_full/
analysis/*/roary_full/
analysis/*/full_pangenome.log
analysis/*/scoary_full/results/
analysis/*/eggnog/cog_db/
analysis/*/eggnog/results/pangenome_vs_cog.tsv
analysis/*/eggnog/db/
analysis/*/eggnog/run.log
analysis/*/eggnog/pangenome_reps.faa
analysis/*/eggnog/pangenome_reps.tsv
analysis/*/abricate_full/
analysis/*/abricate_full.log
analysis/*/phylogeny_full/_genes_unaligned/
analysis/*/phylogeny_full/_genes_aligned/
analysis/*/phylogeny_full/core_supermatrix.fna
analysis/*/phylogeny_full/iqtree.log
analysis/*/phylogeny_full/iqtree_full.iqtree
analysis/*/phylogeny_full/iqtree_full.log
analysis/*/phylogeny_full/iqtree_full.mldist
analysis/*/phylogeny_full/iqtree_full.splits.nex
analysis/*/phylogeny_full/iqtree_full.uniqueseq.phy
analysis/*/phylogeny_full/iqtree_full.bionj
analysis/*/phylogeny_full/iqtree_full.contree
analysis/*/phylogeny_full/iqtree_full.ckp.gz
analysis/*/cafe/results/Base_asr.tre
analysis/*/cafe/results/Base_branch_probabilities.tab
analysis/*/cafe/results/Base_change.tab
analysis/*/cafe/results/Base_count.tab
analysis/*/cafe/results/Base_report.cafe
analysis/*/cafe/tree_ultrametric.nwk
examples/_stage_demo_ws/
examples/_cache_demo_ws/
examples/_parallel_demo_ws/
examples/_pipeline_demo_ws/
analysis/*/pangenome_via_sdk/
analysis/*/pangenome_sdk_13/
analysis/*/sdk_13_run.log
analysis/*/.cache/
examples/_pectobacterium_ws/
examples/_pectobacterium_run.log

# Update scheduler outputs (per-machine, not for version control)
update/notifications/
update/last_run.json
update/release_watch_state.json
update/notifications/cron.log
update/notifications/release_watch.log

# Build artifacts
dist/
build/
*.egg-info/

# MkDocs build output
site/
