.gitignore
LICENSE
README.md
pyproject.toml
pytest.ini
requirements.txt
setup.cfg
setup.py
.github/workflows/publish.yml
.github/workflows/publish_docs.yml
.github/workflows/tests.yml
.github/workflows/trigger-eva-sub-cli-integration-tests.yml
conda/build.sh
conda/meta.yaml
docker/Dockerfile
docs/README.md
docs/_config.yml
docs/how_to_submit.md
docs/input_file_overview.md
docs/installation.md
docs/using_nextflow.md
docs/validation_overview.md
eva_sub_cli/__init__.py
eva_sub_cli/_version.py
eva_sub_cli/auth.py
eva_sub_cli/date_utils.py
eva_sub_cli/file_utils.py
eva_sub_cli/metadata.py
eva_sub_cli/orchestrator.py
eva_sub_cli/report.py
eva_sub_cli/semantic_metadata.py
eva_sub_cli/submission_ws.py
eva_sub_cli/submit.py
eva_sub_cli/utils.py
eva_sub_cli.egg-info/PKG-INFO
eva_sub_cli.egg-info/SOURCES.txt
eva_sub_cli.egg-info/dependency_links.txt
eva_sub_cli.egg-info/entry_points.txt
eva_sub_cli.egg-info/requires.txt
eva_sub_cli.egg-info/top_level.txt
eva_sub_cli/etc/EVA_Submission_Example.xlsx
eva_sub_cli/etc/EVA_Submission_template.xlsx
eva_sub_cli/etc/eva-biosamples.json
eva_sub_cli/etc/eva_logo.png
eva_sub_cli/etc/eva_schema.json
eva_sub_cli/etc/spreadsheet2json_conf.yaml
eva_sub_cli/etc/spreadsheet2json_conf_V2.yaml
eva_sub_cli/exceptions/__init__.py
eva_sub_cli/exceptions/invalid_file_type_exception.py
eva_sub_cli/exceptions/metadata_template_version_exception.py
eva_sub_cli/exceptions/submission_not_found_exception.py
eva_sub_cli/exceptions/submission_status_exception.py
eva_sub_cli/exceptions/submission_upload_exception.py
eva_sub_cli/executables/__init__.py
eva_sub_cli/executables/check_fasta_insdc.py
eva_sub_cli/executables/check_metadata_semantics.py
eva_sub_cli/executables/cli.py
eva_sub_cli/executables/evidence_type_checker.py
eva_sub_cli/executables/samples_checker.py
eva_sub_cli/executables/trim_down.py
eva_sub_cli/executables/xlsx2json.py
eva_sub_cli/jinja_templates/html/fasta_check.html
eva_sub_cli/jinja_templates/html/file_validation.html
eva_sub_cli/jinja_templates/html/metadata_validation.html
eva_sub_cli/jinja_templates/html/project_details.html
eva_sub_cli/jinja_templates/html/report.html
eva_sub_cli/jinja_templates/html/sample_name_check.html
eva_sub_cli/jinja_templates/html/shallow_validation.html
eva_sub_cli/jinja_templates/text/fasta_check.txt
eva_sub_cli/jinja_templates/text/file_validation.txt
eva_sub_cli/jinja_templates/text/metadata_validation.txt
eva_sub_cli/jinja_templates/text/project_details.txt
eva_sub_cli/jinja_templates/text/report.txt
eva_sub_cli/jinja_templates/text/sample_name_check.txt
eva_sub_cli/jinja_templates/text/shallow_validation.txt
eva_sub_cli/nextflow/validation.nf
eva_sub_cli/validators/__init__.py
eva_sub_cli/validators/docker_validator.py
eva_sub_cli/validators/native_validator.py
eva_sub_cli/validators/validation_results_parsers.py
eva_sub_cli/validators/validator.py
tests/build_and_test_docker_locally.py
tests/ignore_test_nextflow_validation.yml
tests/test_auth.py
tests/test_check_fasta_insdc.py
tests/test_cli.py
tests/test_docker_validator.py
tests/test_evidence_type_checker.py
tests/test_file_utils.py
tests/test_metadata.py
tests/test_orchestrator.py
tests/test_report.py
tests/test_samples_checker.py
tests/test_semantic_metadata.py
tests/test_submit.py
tests/test_trim_down.py
tests/test_utils.py
tests/test_validaton_results_parsers.py
tests/test_validator.py
tests/test_xlsx2json.py
tests/resources/EVA_Submission_Docker_Test.xlsx
tests/resources/EVA_Submission_test.json
tests/resources/EVA_Submission_test.xlsx
tests/resources/EVA_Submission_test_V2.xlsx
tests/resources/EVA_Submission_test_fails.xlsx
tests/resources/EVA_Submission_test_version_missing.xlsx
tests/resources/EVA_Submission_test_with_asm_report.json
tests/resources/EVA_Submission_test_with_project_accession.json
tests/resources/EVA_Submission_test_with_project_accession.xlsx
tests/resources/metadata_with_filename.json
tests/resources/assembly_check/invalid.vcf.assembly_check.log
tests/resources/assembly_check/invalid.vcf.text_assembly_report.txt
tests/resources/assembly_reports/input_passed.txt
tests/resources/fasta_files/Saccharomyces_cerevisiae_I.fa
tests/resources/fasta_files/input_passed.fa
tests/resources/fasta_files/multi_seq.fa
tests/resources/sample_checker/example1.vcf.gz
tests/resources/sample_checker/example2.vcf
tests/resources/sample_checker/example3.vcf
tests/resources/sample_checker/metadata.json
tests/resources/validation_reports/expected_report_metadata_json.html
tests/resources/validation_reports/expected_report_metadata_json.txt
tests/resources/validation_reports/expected_report_metadata_json_process_not_run.html
tests/resources/validation_reports/expected_report_metadata_json_process_not_run.txt
tests/resources/validation_reports/expected_report_metadata_xlsx.html
tests/resources/validation_reports/expected_report_metadata_xlsx.txt
tests/resources/validation_reports/expected_shallow_metadata_xlsx_report.html
tests/resources/validation_reports/expected_shallow_metadata_xlsx_report.txt
tests/resources/validation_reports/validation_output/assembly_check/input_passed.vcf.assembly_check.log
tests/resources/validation_reports/validation_output/assembly_check/input_passed.vcf.text_assembly_report.1680102476700.txt
tests/resources/validation_reports/validation_output/assembly_check/input_passed.vcf.valid_assembly_report.1680102476700.txt
tests/resources/validation_reports/validation_output/other_validations/evidence_type_checker.yml
tests/resources/validation_reports/validation_output/other_validations/input_passed.fa_check.yml
tests/resources/validation_reports/validation_output/other_validations/input_passed_trim_down.yml
tests/resources/validation_reports/validation_output/other_validations/metadata_conversion_errors.yml
tests/resources/validation_reports/validation_output/other_validations/metadata_semantic_check.yml
tests/resources/validation_reports/validation_output/other_validations/metadata_validation.txt
tests/resources/validation_reports/validation_output/other_validations/sample_checker.yml
tests/resources/validation_reports/validation_output/vcf_format/input_passed.vcf.errors.1680102476854.db
tests/resources/validation_reports/validation_output/vcf_format/input_passed.vcf.errors.1680102476854.txt
tests/resources/validation_reports/validation_output/vcf_format/input_passed.vcf.vcf_format.log
tests/resources/vcf_files/example2.vcf.gz
tests/resources/vcf_files/input_passed.vcf