.flake8
.gitignore
.gitlab-ci.yml
CHANGELOG
CODE_OF_CONDUCT.md
CONTRIBUTING.md
LICENSE
README.md
environment.yml
pyproject.toml
setup.py
config/config.yaml
nbitk/__init__.py
nbitk/_version.py
nbitk/config.py
nbitk/logger.py
nbitk.egg-info/PKG-INFO
nbitk.egg-info/SOURCES.txt
nbitk.egg-info/dependency_links.txt
nbitk.egg-info/requires.txt
nbitk.egg-info/top_level.txt
nbitk/Phylo/BOLDXLSXIO.py
nbitk/Phylo/DwCATaxonomyIO.py
nbitk/Phylo/NCBITaxdmp.py
nbitk/Phylo/__init__.py
nbitk/SeqIO/BCDM.py
nbitk/SeqIO/__init__.py
nbitk/Services/MinioS3.py
nbitk/Services/__init__.py
nbitk/Services/BOLD/IDService.py
nbitk/Services/BOLD/TaxonValidator.py
nbitk/Services/Galaxy/BLASTN.py
nbitk/Services/Galaxy/BaseClient.py
nbitk/Services/Galaxy/BaseToolClient.py
nbitk/Services/Galaxy/BaseWorkflowClient.py
nbitk/Services/Galaxy/TaxonValidator.py
nbitk/Services/Galaxy/metabarcoding.py
nbitk/Taxon/__init__.py
nbitk/Taxon/_taxon.py
nbitk/Tools/__init__.py
nbitk/Tools/blastdb_aliastool.py
nbitk/Tools/blastdbcmd.py
nbitk/Tools/blastn.py
nbitk/Tools/cutadapt.py
nbitk/Tools/hmmalign.py
nbitk/Tools/makeblastdb.py
nbitk/Tools/megatree_loader.py
nbitk/Tools/megatree_pruner.py
nbitk/Tools/raxml_ng.py
nbitk/Tools/tool_runner.py
nbitk/Tools/vsearch.py
tests/__init__.py
tests/test_BCDM_parser.py
tests/test_BOLDXSLSXIO_parser.py
tests/test_DwCATaxonomyIO_parser.py
tests/test_NCBITaxdmp_parser.py
tests/test_config.py
tests/test_logger.py
tests/test_regress_cscblast.py
tests/test_taxon.py
tests/data/BCDM.jsonl
tests/data/BCDM.tsv
tests/data/COI-5P.hmm
tests/data/bold.xlsx
tests/data/nsr-20250207.dwca.zip
tests/data/records.json
tests/data/sample_R1.fastq.gz
tests/data/seqidlist.txt
tests/data/test_metabarcoding_client.zip
tests/data/minio_test_folder/test_put_file1.txt
tests/data/minio_test_folder/test_put_file2.txt
tests/data/minio_test_folder/sub_folder/test_put_file3.txt
tests/data/minio_test_folder/sub_folder/sub_sub_folder/test_put_file4.txt
tests/test_services/__init__.py
tests/test_services/bold_test_file.fasta
tests/test_services/test_blast_client.py
tests/test_services/test_bold_client.py
tests/test_services/test_metabarcoding_client.py
tests/test_services/test_minios3.py
tests/test_services/test_taxonval_bold.py
tests/test_services/test_taxonval_client.py
tests/test_tools/test_blastdb_aliastool.py
tests/test_tools/test_blastdbcmd.py
tests/test_tools/test_blastn.py
tests/test_tools/test_cutadapt.py
tests/test_tools/test_hmmalign.py
tests/test_tools/test_makeblastdb.py
tests/test_tools/test_megatree_loader.py
tests/test_tools/test_megatree_pruner.py
tests/test_tools/test_raxml_ng.py
tests/test_tools/test_vsearch.py