.gitignore

# Ignore python cache 
__pycache__/

# Ignore pip install dist/ 
dist/

# Build and Release Folders
bin-debug/
bin-release/
[Oo]bj/
[Bb]in/

# Other files and folders
.settings/

# Executables
*.swf
*.air
*.ipa
*.apk

# Backups tmp
*.bck

# Project files, i.e. `.project`, `.actionScriptProperties` and `.flexProperties`
# should NOT be excluded as they contain compiler settings and other important
# information for Eclipse / Flash Builder.


kegg_genomes/
mgnify_catalogues/
gtdb_kofam_scan_per_module/
seed_complements/
gtdb_genomes/
*.keg

gtdb_metadata_r202.tsv

# Silva - Qiime files 
qiime2_consensus_taxonomy_7_levels.tsv
taxmap_embl_ssu_ref_132.txt


__pycache__/

# Ignore NCBI Taxonomy db and mgnify catalogues metadata provided by the MGNify FTP
mappings/mgnify_mappings/metadata/
ref-dbs/taxdump/
ref-dbs/microbetag_genomes/
microbetagDB/ref-dbs/all_genome_modules/


tools/BugBase/


# Ignore software
tools/phenotrex/


mappings/gtdb_ncbi/gtdb_metadata/gtdb_species2ncbi_ids.tsv
mappings/gtdb_ncbi/qiime2/qiime2species_ncbi_ids.tsv
mappings/gtdb_ncbi/dada2/dada2genera.tsv
mappings/gtdb_ncbi/dada2/dada2species.tsv
mappings/gtdb_ncbi/gtdb_metadata/gtdb_species2ncbi_ids.tsv
mappings/gtdb_ncbi/qiime2/qiime2species_ncbi_ids.tsv

microbetagDB/ref-dbs/ko_per_mod_in_genome_per_ncbiId.json

*.swp

tests/output_dev*
dada2familiesNcbiIds
*.nans
*.ini
*.pckl
*.contigs.fa
bins/

elos_bins.tsv
kos_on_modules_graph.tsv

# Ignore the output of the installation.sh script 
microbetag_env

# Ignore .json files under the scripts folder udner the microbetagDB
microbetagDB/scripts/*.json 

gtdb_16s.RData

gurobi.lic
__pycache__/
.vscode/