bioAF
A self-hosted platform for orchestrating bioinformatics pipelines, managing experimental metadata, and running reproducible compute workloads.
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- ai-guides.mdc
- bug_report.yml
- feature_request.yml
- build.yml
- changelog-check.yml
- ci.yml
- release.yml
- CODEOWNERS
- pull_request_template.md
- domain-language.md
- git-conventions.md
- glossary.md
- grilling-protocol.md
- README.md
- spec-format.md
- tdd.md
- writing-style.md
- bioAF_Architecture.svg
- mascot.png
- 001_initial_schema.py
- 002_phase5_data_viz.py
- 003_phase6_gitops_packages.py
- 004_phase7_ops_polish.py
- 005_add_minseqe_fields_samples.py
- 006_add_minseqe_fields_batches.py
- 007_add_minseqe_fields_pipeline_runs.py
- 008_create_controlled_vocabularies.py
- 009_create_pipeline_run_reviews.py
- 010_update_experiment_status_enum.py
- 011_seed_controlled_vocabularies.py
- 012_create_reference_datasets.py
- 013_create_reference_dataset_files.py
- 014_create_pipeline_run_references.py
- 015_upgrade_projects_table.py
- 016_create_project_samples.py
- 017_add_project_id_to_related_tables.py
- 018_create_analysis_snapshots.py
- 019_add_compute_stack_config.py
- 020_add_naming_profiles_ingest_tables.py
- 021_add_pipeline_trigger_tables.py
- 022_add_gcp_config.py
- 023_phase17_terraform_executor.py
- 024_phase18_gcs_bucket_infra.py
- 025_phase19_compute_stack_deploy.py
- 026_phase20_live_pipeline_execution.py
- 027_phase21_auto_ingest_pubsub.py
- 028_phase22_notebook_k8s_columns.py
- 029_add_gcp_service_account_email.py
- 030_create_experiment_field_defaults.py
- 031_add_budget_currency.py
- 032_create_orphaned_resources.py
- 033_add_file_source_metadata.py
- 034_backfill_file_source_metadata.py
- 035_session_credentials_and_last_login.py
- 036_custom_rbac_permission_tables.py
- 037_versioned_compute_environments.py
- 038_rename_to_compute_sessions.py
- 039_add_work_nodes_configure_permission.py
- 040_add_smtp_credential_columns.py
- 041_add_provenance_fields.py
- 042_seed_design_type_vocabulary.py
- 043_add_code_to_projects_experiments.py
- 044_add_unique_sample_files.py
- 045_backfill_file_project_id_from_experiment.py
- 046_add_pipeline_run_input_files.py
- 047_notebook_output_provenance.py
- 048_add_github_repo_git_columns.py
- 049_add_settings_configure_permission.py
- 050_add_ssh_keys_to_session_credentials.py
- 051_slack_oauth_installation.py
- 052_slack_credentials_on_org.py
- 053_add_storage_deleted_to_files.py
- 054_add_deploy_progress_to_terraform_runs.py
- 055_default_pipeline_machine_to_highmem16.py
- 056_add_access_url_to_cellxgene_publications.py
- 057_notebook_file_lifecycle.py
- 058_manifest_driven_ingest.py
- 059_add_is_required_to_custom_fields.py
- 060_add_sample_custom_fields.py
- 061_setup_wizard_overhaul.py
- 062_add_sequencing_batch_position.py
- 063_add_experiment_auto_run_tables.py
- 064_add_terraform_run_tfvars.py
- 065_add_unique_constraint_platform_config_key.py
- 066_add_failure_reason_to_pipeline_runs.py
- 067_work_node_gce_overhaul.py
- 068_custom_pipelines.py
- 069_files_is_global.py
- 070_add_qc_template_to_pipelines.py
- 071_add_references_resource_permissions.py
- 072_add_reference_import_progress.py
- 073_add_reference_category_to_pipeline_vars.py
- 074_add_column_aliases_to_experiments.py
- 075_add_nf_core_registry.py
- 076_encrypt_sensitive_columns.py
- 077_lims_integration_auth.py
- 078_lims_integration_data_model.py
- 079_lims_integration_webhooks.py
- 080_internal_uuid_and_external_id.py
- 081_llm_integration_v1.py
- 082_llm_section_builder.py
- 083_literature_library.py
- 084_literature_in_library.py
- 085_lit_review_relevance_threshold.py
- 086_literature_automation.py
- 087_backfill_notification_links.py
- 088_dashboard_layouts.py
- 089_add_verification_code_token.py
- 090_networking_settings_defaults.py
- 091_naming_profile_redesign.py
- 092_naming_profile_on_template_and_experiment.py
- 093_default_interactive_machine_to_e2_standard_8.py
- 094_session_failure_taxonomy.py
- 095_lab_documents.py
- 096_lab_glossary.py
- 097_sdr.py
- 098_lab_document_notes.py
- 099_lab_document_url_imports.py
- 100_lab_glossary_experiment_scan.py
- 101_neutral_compute_job_ref.py
- 102_add_storage_uri.py
- 103_assistant_use_permission.py
- 104_assistant_conversation_tables.py
- 105_add_sample_assay.py
- 106_add_assistant_launch_enabled.py
- 107_drop_assistant_launch_enabled.py
- 108_validation_studies.py
- 109_reproduction_plans.py
- 110_validation_study_run_links.py
- 111_reproduction_plan_differential_design.py
- 112_reproduction_plan_finding_claim.py
- 113_pipeline_catalog_input_schema.py
- 114_sample_sex.py
- 115_samplesheet_mappings.py
- 116_pipeline_run_samplesheet_provenance.py
- 117_pipeline_catalog_input_schema_version.py
- 118_samplesheet_mapping_promote_permission.py
- 119_file_sequencing_identity.py
- 120_file_asset_identity.py
- 121_samplesheet_mapping_columns.py
- 122_run_identity_snapshot.py
- 123_file_soft_delete.py
- 124_reproduction_plan_tools.py
- 125_seed_non_mammalian_reference_genomes.py
- 126_widen_comparison_target_unit.py
- 127_reproduction_plan_library_strategy.py
- alembic.ini
- env.py
- __init__.py
- base.py
- gcp.py
- __init__.py
- kubernetes.py
- __init__.py
- aws.py
- base.py
- gcp.py
- __init__.py
- cluster_autoscaler.py
- kubernetes.py
- slurm.py
- __init__.py
- base.py
- credential_injector.py
- gcp.py
- __init__.py
- base.py
- gcp.py
- __init__.py
- aws.py
- base.py
- gcp.py
- __init__.py
- aws.py
- base.py
- gcp.py
- __init__.py
- connection.py
- __init__.py
- base.py
- gcp.py
- __init__.py
- gcs_sync.py
- kubernetes.py
- slurm.py
- __init__.py
- base.py
- gcp.py
- __init__.py
- aws.py
- base.py
- gcp.py
- __init__.py
- base.py
- gcp.py
- __init__.py
- gcs.py
- nfs.py
- s3.py
- __init__.py
- aws.py
- gcp.py
- __init__.py
- ec2.py
- gce.py
- gce_capacity.py
- __init__.py
- base.py
- capabilities.py
- failure_classification.py
- models.py
- registry.py
- __init__.py
- _common.py
- agent_review_config.py
- associations.py
- citations.py
- comments.py
- lit_review_runs.py
- papers.py
- reading_status.py
- recommendations.py
- searches.py
- settings.py
- sources.py
- __init__.py
- dependencies.py
- experiments.py
- files.py
- projects.py
- samples.py
- __init__.py
- __init__.py
- access_logs.py
- activity_feed.py
- agent_reviews.py
- assistant.py
- audit.py
- auth.py
- auto_ingest.py
- aws_config.py
- backups.py
- batches.py
- beta_features.py
- billing_export.py
- bootstrap.py
- cellxgene.py
- components.py
- content_tokens.py
- costs.py
- custom_pipelines.py
- dashboards.py
- data_export.py
- datasets.py
- dependencies.py
- documents.py
- environments.py
- experiment_auto_runs.py
- experiments.py
- files.py
- gcp_config.py
- geo_export.py
- github_repos.py
- gitops.py
- health.py
- infrastructure.py
- ingest.py
- integrations_admin.py
- lab_documents.py
- lab_glossary.py
- llm_config.py
- naming_profiles.py
- networking.py
- notebook_sessions.py
- notebooks.py
- notifications.py
- orphaned_resources.py
- pipeline_run_reviews.py
- pipeline_runs.py
- pipelines.py
- plots.py
- projects.py
- provenance_reports.py
- qc_dashboards.py
- references.py
- roles.py
- router.py
- sample_batches.py
- samples.py
- samplesheet_mappings.py
- sdr.py
- search.py
- sequencing_batches.py
- sheets_import.py
- slack_oauth.py
- snapshots.py
- ssh_connect.py
- stack_deploy.py
- storage.py
- storage_deploy.py
- template_notebooks.py
- templates.py
- terraform_executor.py
- upgrades.py
- users.py
- validation_studies.py
- vocabularies.py
- work_nodes.py
- __init__.py
- __main__.py
- create_admin.py
- register_outputs.py
- rotate_encryption_keys.py
- __init__.py
- auth_middleware.py
- logging_middleware.py
- rate_limit.py
- security_headers.py
- __init__.py
- _storage_uri_sync.py
- access_log.py
- activity_feed.py
- agent_review.py
- agent_review_job.py
- agent_review_prompt.py
- analysis_snapshot.py
- api_key.py
- assistant.py
- audit_log.py
- batch.py
- budget_config.py
- cellxgene_publication.py
- comparison_target.py
- component.py
- controlled_vocabulary.py
- cost_record.py
- custom_pipeline.py
- custom_pipeline_variable.py
- custom_pipeline_version.py
- dashboard.py
- document.py
- entity_snapshot.py
- environment.py
- environment_version.py
- experiment.py
- experiment_auto_run.py
- experiment_custom_field.py
- experiment_field_default.py
- experiment_template.py
- file.py
- file_parse_result.py
- github_repo.py
- gitops_repo.py
- idempotency_key.py
- ingest_event.py
- lab_document.py
- lab_glossary.py
- literature.py
- llm_provider_config.py
- manifest_entry.py
- naming_profile.py
- nf_core_registry_pipeline.py
- nf_core_registry_refresh.py
- notebook_session.py
- notebook_session_file.py
- notification.py
- org_code_counter.py
- organization.py
- orphaned_resource.py
- pending_auto_run.py
- pipeline_catalog_entry.py
- pipeline_cost_history.py
- pipeline_process.py
- pipeline_run.py
- pipeline_run_input_file.py
- pipeline_run_review.py
- pipeline_trigger.py
- plot_archive_entry.py
- project.py
- project_custom_field.py
- project_sample.py
- qc_dashboard.py
- reference_dataset.py
- reference_import_progress.py
- reproduction_plan.py
- role.py
- sample.py
- sample_batch.py
- sample_custom_field.py
- samplesheet_mapping.py
- sdr.py
- sequencing_batch.py
- session_credential.py
- slurm_job.py
- storage_stats.py
- template_notebook.py
- trigger_evaluation.py
- upgrade_history.py
- user.py
- user_quota.py
- validation_study.py
- webhook.py
- __init__.py
- nextflow_trace.py
- bioaf-system-test.json
- nf-core-fetchngs.json
- nf-core-rnaseq.json
- nf-core-scrnaseq.json
- __init__.py
- cloud_provider.py
- encryption_service.py
- platform_config_service.py
- stack_options.py
- work_dir_layout.py
- __init__.py
- common.py
- experiment.py
- file.py
- project.py
- sample.py
- __init__.py
- access_log.py
- activity_feed.py
- analysis_snapshot.py
- audit.py
- auth.py
- aws_config.py
- backup.py
- batch.py
- bootstrap.py
- cellxgene.py
- component.py
- connection.py
- controlled_vocabulary.py
- cost.py
- custom_pipeline.py
- dashboard.py
- data_search.py
- dataset.py
- document.py
- environment.py
- experiment.py
- experiment_auto_run.py
- file.py
- gcp_config.py
- github_repo.py
- gitops.py
- infrastructure.py
- ingest.py
- lab_document.py
- lab_glossary.py
- literature.py
- naming_profile.py
- networking.py
- notebook_session.py
- notification.py
- orphaned_resource.py
- pipeline.py
- pipeline_run.py
- pipeline_run_review.py
- plot_archive.py
- project.py
- provenance.py
- qc_dashboard.py
- reference_dataset.py
- role.py
- sample.py
- sample_batch.py
- samplesheet_mapping.py
- sdr.py
- search.py
- sequencing_batch.py
- session_credential.py
- sheets_import.py
- storage.py
- template.py
- template_notebook.py
- upgrade.py
- user.py
- validation_study.py
- work_node.py
- __init__.py
- checksum_manifest.py
- excel_generator.py
- geo_export_service.py
- geo_template_definition.json
- readme_generator.py
- superseries_export_service.py
- validation.py
- __init__.py
- biorxiv.py
- europepmc.py
- pubmed.py
- semanticscholar.py
- __init__.py
- accession_manifest_service.py
- agent_review_payload.py
- association_service.py
- citation_service.py
- comment_service.py
- dedup.py
- dismissal_service.py
- extraction.py
- fulltext_service.py
- ground_truth_fetch_service.py
- lit_review_auto_service.py
- lit_review_run_service.py
- paper_service.py
- reading_status_service.py
- recommendation_service.py
- search_service.py
- sources_config_service.py
- storage.py
- upload_service.py
- __init__.py
- anthropic_client.py
- gemma_client.py
- google_client.py
- openai_client.py
- tool_use.py
- da_peaks_deseq2.ipynb
- de_bulk_deseq2.ipynb
- de_pseudobulk_deseq2.ipynb
- __init__.py
- email_adapter.py
- in_app.py
- slack_adapter.py
- __init__.py
- csv_renderer.py
- data_gatherer.py
- json_renderer.py
- markdown_renderer.py
- pdf_renderer.py
- report_service.py
- schema.py
- __init__.py
- gcs_helpers.py
- __init__.py
- atacseq.py
- bulk_rnaseq.py
- chipseq.py
- custom.py
- generic.py
- scrnaseq.py
- __init__.py
- multiqc_registry.py
- resolver.py
- roster.py
- __init__.py
- access_log_service.py
- activity_feed_service.py
- agent_review_artifact_builder.py
- agent_review_job_service.py
- agent_review_prompt_builder.py
- agent_review_prompt_service.py
- agent_review_prompts.py
- agent_review_response_parser.py
- agent_review_section_catalog.py
- api_key_service.py
- asset_identity.py
- assistant_availability_service.py
- assistant_loop_service.py
- assistant_tool_catalog.py
- assistant_tool_service.py
- assistant_untrusted.py
- audit_service.py
- auth_service.py
- auto_ingest_gate.py
- auto_run_service.py
- backup_service.py
- batch_service.py
- beta_features_service.py
- billing_export_service.py
- bootstrap_bamtofastq.py
- bootstrap_environments.py
- bootstrap_lab_knowledge.py
- bootstrap_literature.py
- bootstrap_metadata.py
- bootstrap_roles.py
- cellxgene_image_service.py
- cellxgene_service.py
- cluster_quota.py
- cluster_quota_service.py
- code_service.py
- component_queue.py
- component_service.py
- compute_cost_service.py
- cost_service.py
- csv_service.py
- custom_pipeline_service.py
- dashboard_service.py
- data_search_service.py
- dataset_service.py
- document_service.py
- email_service.py
- environment_build_service.py
- environment_service.py
- event_bus.py
- event_types.py
- experiment_service.py
- export_service.py
- fastq_header.py
- fetchngs_ingest_service.py
- file_organization.py
- file_service.py
- file_type_utils.py
- gcp_config.py
- gcs_storage.py
- github_repo_service.py
- gitops_service.py
- google_sheets_service.py
- h5ad_inspector.py
- idempotency_service.py
- image_build_platform.py
- infra_update_service.py
- ingest_service.py
- lab_document_service.py
- lab_document_upload_service.py
- lab_glossary_extraction.py
- lab_glossary_scan_service.py
- lab_glossary_service.py
- llm_models_fetch_service.py
- llm_provider_config_service.py
- llm_provider_models.py
- machine_types.py
- manifest_ingest_service.py
- manifest_parser.py
- naming_profile_parser.py
- naming_profile_service.py
- networking_applier.py
- nf_core_registry_service.py
- notebook_execution_service.py
- notebook_image_service.py
- notebook_service.py
- notification_backfill.py
- notification_router.py
- notification_service.py
- orphaned_resource_service.py
- pipeline_assay_fallback.py
- pipeline_catalog_service.py
- pipeline_mapper.py
- pipeline_monitor_service.py
- pipeline_output_service.py
- pipeline_review_service.py
- pipeline_run_service.py
- plan_parser.py
- plot_archive_service.py
- project_service.py
- provenance_service.py
- pubsub_listener.py
- qc_dashboard_service.py
- quota_service.py
- read_groups.py
- recommend_pipeline_service.py
- reference_data_service.py
- reproduction_plan_service.py
- request_health.py
- result_set_normalizer.py
- role_service.py
- sample_batch_service.py
- sample_completeness_service.py
- sample_service.py
- sample_sheet_service.py
- samplesheet_declaration.py
- samplesheet_mapping_service.py
- samplesheet_schema.py
- sdr_service.py
- search_service.py
- secrets_service.py
- sequencing_enrichment.py
- sequencing_identity.py
- service_account_service.py
- session_bucket.py
- session_credential_service.py
- session_monitor.py
- session_output_service.py
- setup_code_service.py
- sheets_reader_sa_service.py
- slack_oauth_service.py
- slurm_service.py
- snapshot_service.py
- snapshot_utils.py
- stack_deployment.py
- storage_service.py
- template_notebook_service.py
- template_service.py
- terraform_cloud.py
- terraform_executor.py
- thumbnail_service.py
- upgrade_service.py
- upload_service.py
- user_service.py
- validation_classifier_service.py
- validation_concordance_service.py
- validation_driver_service.py
- validation_extraction_service.py
- validation_fetch_reaper.py
- validation_level3_service.py
- validation_sample_values.py
- validation_study_service.py
- vocabulary_validator.py
- webhook_dispatcher.py
- webhook_service.py
- webhook_worker.py
- work_dir_reaper.py
- work_node_service.py
- __init__.py
- review_reminder.py
- __init__.py
- reference_importer.py
- __init__.py
- config.py
- database.py
- error_handlers.py
- exceptions.py
- gcp_zones.py
- logging_config.py
- main.py
- types.py
- url_utils.py
- main.tf
- outputs.tf
- variables.tf
- .terraform.lock.hcl
- main.tf
- outputs.tf
- variables.tf
- .terraform.lock.hcl
- main.tf
- outputs.tf
- variables.tf
- .terraform.lock.hcl
- main.tf
- outputs.tf
- variables.tf
- main.tf
- outputs.tf
- variables.tf
- main.tf
- outputs.tf
- variables.tf
- main.tf
- outputs.tf
- variables.tf
- main.tf
- outputs.tf
- variables.tf
- literature_route_table.golden.json
- atacseq_run24.json
- bulk_rnaseq_run17.json
- chipseq_run22.json
- generic_run34.json
- README.md
- scrnaseq_run11.json
- ampliseq.json
- bacass.json
- demo.json
- funcscan.json
- genomeqc.json
- mag.json
- MANIFEST.json
- raredisease.json
- README.md
- rnasplice.json
- rnastructurome.json
- sarek.json
- taxprofiler.json
- nf_core_pipelines_sample.json
- nf_core_pipelines_sarek_archived.json
- __init__.py
- conftest.py
- test_access_logs.py
- test_accession_manifest.py
- test_activity_feed.py
- test_adapter_models.py
- test_adapters.py
- test_admin_user_management.py
- test_agent_review_artifact_builder.py
- test_agent_review_builder_api.py
- test_agent_review_job_service.py
- test_agent_review_prompt_builder.py
- test_agent_review_prompt_service.py
- test_agent_review_response_parser.py
- test_agent_reviews_api.py
- test_api_keys.py
- test_asset_identity.py
- test_assistant_api.py
- test_assistant_availability.py
- test_assistant_loop_service.py
- test_assistant_models.py
- test_assistant_tool_service.py
- test_assistant_untrusted.py
- test_audit.py
- test_auth.py
- test_auto_ingest_api.py
- test_auto_ingest_neutralized.py
- test_aws_config_api.py
- test_aws_config_schemas.py
- test_aws_validation_adapter.py
- test_backups.py
- test_bal_layering.py
- test_batch_code_resolve.py
- test_batch_position.py
- test_batches.py
- test_beta_features.py
- test_billing_export.py
- test_billing_provider.py
- test_bootstrap.py
- test_bootstrap_bamtofastq.py
- test_bootstrap_environments.py
- test_bootstrap_metadata.py
- test_bootstrap_roles_assistant.py
- test_bootstrap_roles_llm.py
- test_bootstrap_setup_code.py
- test_bucket_naming_invariant.py
- test_build_status_endpoint.py
- test_capabilities_bootstrap.py
- test_capability_guards.py
- test_cellxgene.py
- test_cellxgene_image_service_aws.py
- test_cloud_logging.py
- test_cloud_provider_policy.py
- test_cluster_auth_provider.py
- test_cluster_autoscaler_ensure.py
- test_cluster_autoscaler_manifests.py
- test_cluster_quota.py
- test_cluster_quota_api.py
- test_cluster_quota_reader.py
- test_cluster_status.py
- test_code_service.py
- test_component_catalog_invariants.py
- test_component_queue_orchestrator.py
- test_component_toggle_audit.py
- test_component_toggle_image_build.py
- test_components.py
- test_components_select_batch.py
- test_compute_naming_invariant.py
- test_compute_terraform.py
- test_connection_setup_guide.py
- test_content_tokens.py
- test_costs.py
- test_create_admin.py
- test_credential_injector.py
- test_credentials_provider.py
- test_csv_preview.py
- test_csv_upload.py
- test_custom_pipeline_cascade.py
- test_custom_pipeline_launch.py
- test_custom_pipeline_qc_config.py
- test_custom_pipeline_reference_param.py
- test_custom_pipelines.py
- test_custom_pipelines_api.py
- test_dashboard.py
- test_data_export.py
- test_data_search_api.py
- test_data_search_service.py
- test_datasets.py
- test_deploy_progress.py
- test_docker_compose_config.py
- test_documents.py
- test_domain_error_handler.py
- test_domain_exceptions.py
- test_emitted_name_matching.py
- test_encrypted_model_columns.py
- test_encrypted_string.py
- test_encryption_migration.py
- test_encryption_service.py
- test_entity_snapshots.py
- test_environment_build_aws.py
- test_environments.py
- test_experiment_auto_runs.py
- test_experiment_field_defaults.py
- test_experiments.py
- test_fastq_header.py
- test_fastq_header_on_ingest.py
- test_fetchngs_accessions_run_path.py
- test_fetchngs_ingest.py
- test_file_asset_identity.py
- test_file_delete_frees_storage.py
- test_file_download.py
- test_file_global_scope.py
- test_file_inheritance.py
- test_file_organization.py
- test_file_provenance.py
- test_file_sequencing_identity.py
- test_file_soft_delete.py
- test_file_stats.py
- test_file_type_utils.py
- test_files.py
- test_full_search.py
- test_full_search_api.py
- test_fulltext_fetch.py
- test_gce_adapter.py
- test_gcp_config_api.py
- test_gcp_config_dual_probe.py
- test_gcp_config_migration.py
- test_gcp_config_response_bootstrap_email.py
- test_gcp_config_schemas.py
- test_gcp_config_service.py
- test_gcs_object_store.py
- test_gcs_storage_adapter.py
- test_gcs_storage_adapter_pipeline.py
- test_gcs_storage_service.py
- test_geo_checksum_readme.py
- test_geo_excel.py
- test_geo_export_api.py
- test_geo_export_service.py
- test_geo_validation.py
- test_git_pod_integration.py
- test_github_db_columns.py
- test_gitops.py
- test_gke_connection.py
- test_gke_tag_invariant.py
- test_google_sheets_service.py
- test_ground_truth_fetch.py
- test_iam_provider.py
- test_illumina_filename_parsing.py
- test_image_build_credentials.py
- test_image_build_platform.py
- test_image_build_provider.py
- test_image_registry_provider.py
- test_info_disclosure.py
- test_infra_update_api.py
- test_infra_update_service.py
- test_infrastructure_api.py
- test_infrastructure_components.py
- test_ingest_api.py
- test_ingest_credentials_passthrough.py
- test_ingest_pipeline_bugs.py
- test_ingest_real_gcs.py
- test_ingest_service.py
- test_integrations_admin.py
- test_integrations_experiments.py
- test_integrations_files.py
- test_integrations_openapi.py
- test_integrations_projects.py
- test_integrations_samples.py
- test_jwt_secret_validation.py
- test_k8s_adapter.py
- test_k8s_adapter_sa_hardening.py
- test_k8s_cellxgene_adapter.py
- test_k8s_cluster_metrics_cost.py
- test_k8s_compute_adapter.py
- test_k8s_gcs_credentials.py
- test_k8s_gke_auth.py
- test_k8s_job_operations.py
- test_k8s_job_ttl.py
- test_k8s_label_sanitize.py
- test_k8s_log_fallback.py
- test_k8s_metrics_from_config.py
- test_k8s_namespace_ensure.py
- test_k8s_namespace_setup.py
- test_k8s_nextflow_job.py
- test_k8s_notebook_adapter.py
- test_k8s_notebook_headless.py
- test_k8s_notebook_launch.py
- test_k8s_outofcluster_auth.py
- test_k8s_run_report.py
- test_k8s_session_credentials.py
- test_k8s_submit_job.py
- test_k8s_termination_message.py
- test_lab_document_service.py
- test_lab_document_ssrf_guard.py
- test_lab_documents_api.py
- test_lab_documents_model.py
- test_lab_documents_search.py
- test_lab_glossary_api.py
- test_lab_glossary_scan_phase_d.py
- test_lab_glossary_scan_service.py
- test_lab_glossary_search.py
- test_lab_glossary_term_service.py
- test_lab_knowledge_rbac.py
- test_level3_templates.py
- test_literature_agent_review.py
- test_literature_api.py
- test_literature_api_schemas.py
- test_literature_automation.py
- test_literature_extraction.py
- test_literature_lit_review_run.py
- test_literature_router_structure.py
- test_literature_schema.py
- test_literature_search_api.py
- test_literature_upload_api.py
- test_llm_config_api.py
- test_llm_provider_client_errors.py
- test_llm_provider_config.py
- test_llm_provider_models_fetch.py
- test_log_redaction.py
- test_manifest_file_reconciliation.py
- test_manifest_ingest.py
- test_manifest_parser.py
- test_manifest_position_resolve.py
- test_manifest_reconciliation.py
- test_migration_023.py
- test_migration_024.py
- test_migration_025.py
- test_migration_026.py
- test_migration_081.py
- test_migration_093.py
- test_migration_101.py
- test_migrations_apply.py
- test_naming_profile_api.py
- test_naming_profile_models.py
- test_naming_profile_on_template_and_experiment.py
- test_naming_profile_parser.py
- test_naming_profile_service.py
- test_networking_api.py
- test_networking_applier.py
- test_nextflow_igenomes_ignore.py
- test_nextflow_k8s_executor.py
- test_nextflow_profile_and_defaults.py
- test_nextflow_trace.py
- test_nf_core_registry.py
- test_nfs_storage_adapter.py
- test_notebook_api_v1.py
- test_notebook_execution.py
- test_notebook_file_mounting.py
- test_notebook_gcs_bucket.py
- test_notebook_gcs_sync.py
- test_notebook_image_service.py
- test_notebook_output_discovery.py
- test_notebook_output_provenance.py
- test_notebook_session_sync.py
- test_notebook_sessions_v1.py
- test_notebooks.py
- test_notifications.py
- test_observability_provider.py
- test_openapi_exposure.py
- test_orphaned_recovery.py
- test_orphaned_resources.py
- test_output_uid_matching.py
- test_packages_removed.py
- test_packer_template_disk.py
- test_persist_cloud_provider.py
- test_phase13_schemas.py
- test_phase21_migration.py
- test_phase22_migration.py
- test_phase22_terraform.py
- test_phase23_files.py
- test_pipeline_assay_fallback.py
- test_pipeline_catalog.py
- test_pipeline_io_lineage.py
- test_pipeline_launcher.py
- test_pipeline_mapper.py
- test_pipeline_monitor.py
- test_pipeline_monitor_custom.py
- test_pipeline_monitor_oom.py
- test_pipeline_monitor_preemption.py
- test_pipeline_monitor_read_storage.py
- test_pipeline_output_service.py
- test_pipeline_output_visibility.py
- test_pipeline_reference_linkage.py
- test_pipeline_results_bucket.py
- test_pipeline_run_jobspec.py
- test_pipeline_run_missing_files.py
- test_pipeline_run_neutral_fields.py
- test_pipeline_run_preflight.py
- test_pipeline_run_preview_api.py
- test_pipeline_run_reviews.py
- test_pipeline_run_samplesheet_contract.py
- test_pipeline_run_samplesheet_provenance.py
- test_pipeline_runs.py
- test_pipeline_runs_sorting.py
- test_pipeline_task_pod_isolation.py
- test_pipeline_trigger_models.py
- test_pipeline_unschedulable.py
- test_plan_parser.py
- test_platform_config_guard.py
- test_platform_config_service.py
- test_plot_archive_fixes.py
- test_plots.py
- test_pod_identity_provider.py
- test_projects.py
- test_provenance.py
- test_provenance_fields.py
- test_provenance_report_api.py
- test_provenance_reports.py
- test_provider_capabilities.py
- test_pubsub_listener.py
- test_pubsub_manifest_routing.py
- test_qc_atacseq_extractor.py
- test_qc_bulk_rnaseq_extractor.py
- test_qc_chipseq_extractor.py
- test_qc_dashboard.py
- test_qc_dashboard_api_config.py
- test_qc_dashboard_template_dispatch.py
- test_qc_generic_metrics_are_qc_floor.py
- test_qc_generic_routing.py
- test_qc_generic_template.py
- test_qc_multiqc_registry.py
- test_qc_per_sample_depth.py
- test_qc_plot_upload.py
- test_qc_real_multiqc_regression.py
- test_qc_roster_for_run.py
- test_qc_scrnaseq_extractor.py
- test_qc_template_fields.py
- test_qc_template_resolver.py
- test_qc_templates.py
- test_queue_lifecycle_hooks.py
- test_quick_search.py
- test_rate_limit_proxy.py
- test_read_groups.py
- test_recommend_pipeline_service.py
- test_reference_by_name.py
- test_reference_data.py
- test_reference_file_type_detector.py
- test_reference_filter_options.py
- test_reference_genome_autopopulate.py
- test_reference_genome_vocabulary.py
- test_reference_import_progress_model.py
- test_reference_import_routes.py
- test_reference_import_service.py
- test_reference_importer_worker.py
- test_reference_upload_complete.py
- test_reference_upload_complete_route.py
- test_reference_upload_init.py
- test_reference_upload_init_route.py
- test_references_resource_permissions.py
- test_register_outputs_cli.py
- test_registry_backends.py
- test_reproduction_plan_service.py
- test_request_health.py
- test_result_set_normalizer.py
- test_role_service.py
- test_roles_api.py
- test_roles_manifest.py
- test_rotate_encryption_keys.py
- test_run_failure_excerpt.py
- test_run_samplesheet_provenance_api.py
- test_s3_storage_adapter.py
- test_sample_batch_rename.py
- test_sample_completeness_trigger.py
- test_sample_sex_optional.py
- test_sample_sheet.py
- test_sample_sheet_auto_files.py
- test_sample_sheet_column_order.py
- test_sample_sheet_exclusive_columns.py
- test_sample_sheet_file_columns.py
- test_sample_sheet_per_sample_values.py
- test_sample_sheet_regression_lock.py
- test_sample_sheet_safe_names.py
- test_sample_sheet_schema_driven.py
- test_samples.py
- test_samplesheet_contract_refresh.py
- test_samplesheet_declaration.py
- test_samplesheet_declared_launch.py
- test_samplesheet_dependent_columns.py
- test_samplesheet_enum_values.py
- test_samplesheet_launch_blocking.py
- test_samplesheet_mapping_api.py
- test_samplesheet_mappings.py
- test_samplesheet_name_sanitization.py
- test_samplesheet_per_sample_inputs.py
- test_samplesheet_preview.py
- test_samplesheet_row_completeness.py
- test_samplesheet_run_column.py
- test_samplesheet_schema.py
- test_samplesheet_schema_acquisition.py
- test_samplesheet_sequencing_facts.py
- test_samplesheet_uniqueness.py
- test_samplesheet_user_inputs.py
- test_samplesheet_write_back.py
- test_sdr_api.py
- test_sdr_search.py
- test_sdr_service.py
- test_search.py
- test_secrets_provider.py
- test_security_headers.py
- test_sequencing_batch.py
- test_service_bal_integration.py
- test_session_credentials.py
- test_session_failure_classification.py
- test_session_failure_taxonomy.py
- test_session_monitor.py
- test_setup_code.py
- test_setup_code_service.py
- test_sheets_import_api.py
- test_sheets_reader_sa_service.py
- test_slack_oauth.py
- test_slurm_guard.py
- test_smtp_settings.py
- test_snapshots.py
- test_ssh_connect.py
- test_stack_api.py
- test_stack_deploy_background.py
- test_stack_deployment.py
- test_stack_options.py
- test_storage.py
- test_storage_api.py
- test_storage_provider_contract.py
- test_storage_staging_image.py
- test_storage_terraform.py
- test_storage_uri_read_paths.py
- test_storage_uri_sync_shim.py
- test_storage_uri_synonym.py
- test_submit_with_tools.py
- test_superseries_export.py
- test_system_test_pipeline.py
- test_template_notebooks.py
- test_templates.py
- test_terraform_api.py
- test_terraform_cloud.py
- test_terraform_executor.py
- test_terraform_init.py
- test_terraform_legacy_removed.py
- test_terraform_single_owner.py
- test_upgrades.py
- test_upload_credentials_sa_hardening.py
- test_upload_events.py
- test_upload_ingest_bucket.py
- test_users.py
- test_validation_api.py
- test_validation_c1_gate.py
- test_validation_classifier.py
- test_validation_classifier_concordance.py
- test_validation_concordance.py
- test_validation_deposit_conflict.py
- test_validation_design_edit.py
- test_validation_driver.py
- test_validation_driver_backhalf.py
- test_validation_driver_reproducing.py
- test_validation_error_notice.py
- test_validation_extraction.py
- test_validation_fetch_reaper.py
- test_validation_finding_claim.py
- test_validation_level3_wiring.py
- test_validation_provenance.py
- test_validation_sample_values.py
- test_validation_study_service.py
- test_validation_study_state_machine.py
- test_vm_instance_seam.py
- test_vocabularies.py
- test_vocabulary_validation.py
- test_webhooks.py
- test_work_dir_reaper.py
- test_work_node_ec2.py
- test_work_nodes.py
- test_worknode_zone_capacity.py
- test_yaml_parsing.py
- test_zone_capacity_probe.py
- entrypoint.sh
- pyproject.toml
- requirements-dev.txt
- requirements.txt
- uv.lock
- .gitkeep
- README.md
- __init__.py
- deploy.py
- destroy.py
- __init__.py
- checks.py
- __init__.py
- gcp.py
- output.py
- __init__.py
- main.py
- pyproject.toml
- ADR-001-gcp-only.md
- ADR-002-mandatory-optional-split.md
- ADR-003-email-based-auth.md
- ADR-004-tiered-backup-strategy.md
- ADR-005-github-based-upgrades.md
- ADR-006-experiment-tracking-as-foundation.md
- ADR-007-ui-driven-terraform.md
- ADR-008-secret-manager.md
- ADR-009-immutable-audit-log.md
- ADR-010-notification-system.md
- ADR-011-scrna-seq-initial-scope.md
- ADR-012-data-portability.md
- ADR-013-minseqe-compliant-metadata.md
- ADR-014-geo-export-service.md
- ADR-015-analysis-snapshot-sdk.md
- ADR-016-snapshot-comparison-ui.md
- ADR-017-reference-data-management.md
- ADR-018-cross-experiment-projects.md
- ADR-019-pipeline-review-handoff.md
- ADR-020-bioaf-adapter-layer.md
- ADR-021-kubernetes-compute-backend.md
- ADR-022-gcs-storage-backend.md
- ADR-023-cro-naming-profiles.md
- ADR-024-gcs-auto-ingest.md
- ADR-025-automated-pipeline-triggering.md
- ADR-026-ssh-access.md
- ADR-027-navigation-restructure.md
- ADR-028-bigquery-billing-export.md
- ADR-029-signed-url-direct-upload.md
- ADR-030-session-credentials-pam-auth.md
- ADR-031-notebook-image-build-pipeline.md
- ADR-032-custom-rbac.md
- ADR-033-versioned-compute-environments.md
- ADR-034-custom-work-nodes.md
- ADR-035-bioaf-cli.md
- ADR-036-data-export-download.md
- ADR-037-provenance-reporting.md
- ADR-038-pipeline-io-lineage-junction.md
- ADR-039-notebook-output-provenance.md
- ADR-040-notebook-file-lifecycle.md
- ADR-041-environment-build-versioning.md
- ADR-042-spot-preemption-retry-strategy.md
- ADR-043-work-nodes-gce-migration.md
- ADR-044-custom-pipelines.md
- ADR-045-pipeline-environments.md
- ADR-046-pipeline-version-cascade.md
- ADR-047-data-at-rest-encryption.md
- ADR-048-public-integration-api-surface.md
- ADR-049-service-accounts-and-api-keys.md
- ADR-050-external-ids-and-idempotent-writes.md
- ADR-051-outbound-webhook-delivery.md
- ADR-052-llm-integration-trust-boundary.md
- ADR-053-llm-provider-abstraction.md
- ADR-054-gemma-per-request-inference.md
- ADR-055-agent-review-advisory-entity.md
- ADR-056-literature-library-domain-model.md
- ADR-057-literature-as-input-to-agent-review.md
- ADR-058-naming-profile-parse-only.md
- ADR-059-lab-knowledge-institutional-memory.md
- ADR-060-lab-document-tag-organization.md
- ADR-061-lab-document-versioning.md
- ADR-062-glossary-ai-population-human-review.md
- ADR-063-sdr-status-machine.md
- ADR-064-sdr-reassessment-triggers.md
- ADR-065-bal-normalized-contract.md
- ADR-066-terraform-single-execution-owner.md
- ADR-067-conversational-assistant.md
- ADR-068-literature-validation-reproduction-triage.md
- ADR-069-level3-finding-concordance.md
- README.md
- .env.example
- bioaf-update-agent.service
- docker-compose.dev.yml
- docker-compose.yml
- Dockerfile.backend
- Dockerfile.bioaf-scrna
- Dockerfile.cellxgene
- Dockerfile.frontend
- nginx.conf
- ops-agent-config.yaml
- auth.md
- conventions.md
- experiments.md
- files.md
- projects.md
- README.md
- samples.md
- webhooks.md
- analysis-snapshots.md
- automated-pipelines.md
- compute-stack-setup.md
- cross-experiment-projects.md
- custom-pipelines.md
- custom-qc-config.md
- geo-export.md
- naming-profiles.md
- paper-validation.md
- reference-data.md
- ssh-access.md
- adr-index.md
- deploy-demo-deprecation.md
- deployment-guide.md
- life-after-bioaf.md
- README.md
- user-guide-admin.md
- user-guide-bench.md
- user-guide-compbio.md
- backup-recovery.png
- cellxgene.png
- cost-center.png
- dashboard.png
- experiments.png
- files.png
- infrastructure.png
- notebooks.png
- pipeline-catalog.png
- pipeline-runs.png
- qc-dashboards.png
- roles.png
- users.png
- bioAF-logo.svg
- a11y-clickable-elements.test.ts
- a11y-dialog-escape.test.ts
- a11y-file-inputs.test.ts
- a11y-form-labels.test.ts
- a11y-reduced-motion.test.ts
- a11y-table-semantics.test.ts
- a11y-text-contrast.test.ts
- app-shell-boot-failure.test.tsx
- app-shell-surface.test.ts
- brand-contrast.test.ts
- browser-only-modules.test.ts
- buttons-on-button.test.ts
- dark-theme-tokens.test.ts
- dashboard-widget-retry.test.ts
- design-system-adoption.test.ts
- destructive-actions-confirm.test.ts
- document-title-owner.test.ts
- failed-reads-are-not-findings.test.ts
- failure-states-recover.test.tsx
- GettingStarted.test.tsx
- nav-label-agreement.test.ts
- page-descriptions.test.ts
- page-overlays-on-shell.test.ts
- panels-on-card.test.ts
- pdf-hardening.test.ts
- responsive-table-scroll.test.ts
- SetupWizard.test.tsx
- status-registry-adoption.test.ts
- ui-error-copy.test.ts
- page.errors.test.tsx
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- clusterQuotaVerdict.test.ts
- clusterQuotaVerdict.ts
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- AccountTab.test.tsx
- AccountTab.tsx
- NotificationsTab.test.tsx
- NotificationsTab.tsx
- SessionCredentialsTab.test.tsx
- SessionCredentialsTab.tsx
- SSHKeyTab.test.tsx
- SSHKeyTab.tsx
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- page.tsx
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- ApiActivityTab.tsx
- PasswordResetActions.test.tsx
- PasswordResetActions.tsx
- RevealSecretModal.tsx
- ServiceAccountsTab.tsx
- WebhooksTab.tsx
- page.tsx
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- page.errors.test.tsx
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- error.test.tsx
- error.tsx
- layout.test.tsx
- layout.tsx
- page.test.tsx
- page.tsx
- page.test.tsx
- page.tsx
- page.tsx
- page.tsx
- page.errors.test.tsx
- page.test.tsx
- page.tsx
- page.tsx
- favicon.ico
- globals.css
- layout.tsx
- not-found.test.tsx
- not-found.tsx
- AgentReviewButtons.test.tsx
- AgentReviewButtons.tsx
- AgentReviewTab.tsx
- AssembledPromptModal.tsx
- reviewItems.tsx
- SectionBuilderModal.tsx
- AssistantChat.test.tsx
- AssistantChat.tsx
- AssistantLauncher.test.tsx
- AssistantLauncher.tsx
- assistantUiStore.test.ts
- assistantUiStore.ts
- FloatingAssistant.test.tsx
- FloatingAssistant.tsx
- PlanConfirmCard.test.tsx
- PlanConfirmCard.tsx
- InviteForm.tsx
- LoginForm.test.tsx
- LoginForm.tsx
- SetupWizard.test.tsx
- SetupWizard.tsx
- AutoIngestControls.tsx
- ComponentPicker.tsx
- StorageSection.tsx
- TerraformPlanViewer.tsx
- ActivityFeedWidget.tsx
- AutoIngestActivityWidget.test.tsx
- AutoIngestActivityWidget.tsx
- BackupStatusWidget.test.tsx
- BackupStatusWidget.tsx
- CostBudgetWidget.tsx
- CostTrendWidget.test.tsx
- CostTrendWidget.tsx
- DashboardContent.test.tsx
- DashboardContent.tsx
- DashboardWidgetPicker.test.tsx
- DashboardWidgetPicker.tsx
- ExperimentsStatusWidget.test.tsx
- ExperimentsStatusWidget.tsx
- FailedRunsWidget.test.tsx
- FailedRunsWidget.tsx
- InfrastructureHealthWidget.tsx
- IngestStatusWidget.test.tsx
- IngestStatusWidget.tsx
- MyCustomPipelinesWidget.test.tsx
- MyCustomPipelinesWidget.tsx
- MyReadingListWidget.test.tsx
- MyReadingListWidget.tsx
- MySessionsWidget.test.tsx
- MySessionsWidget.tsx
- PendingInvitesWidget.test.tsx
- PendingInvitesWidget.tsx
- QueueDepthWidget.tsx
- RecentLiteratureWidget.test.tsx
- RecentLiteratureWidget.tsx
- RecentPlotsWidget.test.tsx
- RecentPlotsWidget.tsx
- registry.test.ts
- registry.tsx
- RunningJobsWidget.tsx
- RunsAwaitingReviewWidget.test.tsx
- RunsAwaitingReviewWidget.tsx
- TeamOutputWidget.test.tsx
- TeamOutputWidget.tsx
- time.test.ts
- time.ts
- useDashboardLayout.ts
- widget-failure-is-not-data.test.tsx
- DatasetBrowser.tsx
- AutoRunConfigSection.tsx
- CsvUploadModal.tsx
- DataExportModal.tsx
- ExperimentStatusBadge.tsx
- GeoExportModal.tsx
- ReviewBadge.tsx
- ReviewPanel.errors.test.tsx
- ReviewPanel.tsx
- SampleQCBadge.tsx
- SheetImportModal.tsx
- TemplateSheetImportModal.tsx
- ExperimentFileUploader.test.tsx
- ExperimentFileUploader.tsx
- FileBrowser.test.tsx
- FileBrowser.tsx
- BillingSetupModal.tsx
- BootstrapCard.tsx
- DeploymentBanner.test.tsx
- DeploymentBanner.tsx
- DeployProgressModal.tsx
- DeployRecoveryModal.test.tsx
- DeployRecoveryModal.tsx
- InfraUpdatesCard.test.tsx
- InfraUpdatesCard.tsx
- OrphanedResourcesCard.tsx
- TerraformProgressModal.tsx
- TerraformRunHistory.tsx
- LabDocumentBrowser.test.tsx
- LabDocumentBrowser.tsx
- LabDocumentViewer.test.tsx
- LabDocumentViewer.tsx
- LabGlossaryBrowser.test.tsx
- LabGlossaryBrowser.tsx
- SdrBrowser.test.tsx
- SdrBrowser.tsx
- BootSplash.tsx
- Breadcrumb.tsx
- DocumentTitle.test.tsx
- DocumentTitle.tsx
- GlobalSearch.test.tsx
- GlobalSearch.tsx
- Header.test.tsx
- Header.tsx
- navIcons.tsx
- NavItem.tsx
- QuickCreateMenu.test.tsx
- QuickCreateMenu.tsx
- SectionIndex.test.tsx
- SectionIndex.tsx
- Sidebar.test.tsx
- Sidebar.tsx
- AiLitReviewLauncher.test.tsx
- AiLitReviewLauncher.tsx
- AssociatePaperModal.test.tsx
- AssociatePaperModal.tsx
- LiteratureTabPanel.test.tsx
- LiteratureTabPanel.tsx
- PaperPdfViewer.test.tsx
- PaperPdfViewer.tsx
- SearchProgress.test.tsx
- SearchProgress.tsx
- NamingProfileDetail.test.tsx
- NamingProfileDetail.tsx
- NamingProfileSelect.tsx
- NamingProfileWizard.test.tsx
- NamingProfileWizard.tsx
- FileTreeSelector.test.tsx
- FileTreeSelector.tsx
- NotificationBell.errors.test.tsx
- NotificationBell.tsx
- NotificationDropdown.tsx
- NotificationItem.test.tsx
- NotificationItem.tsx
- GettingStarted.tsx
- CustomPipelineLaunchDialog.test.tsx
- CustomPipelineLaunchDialog.tsx
- LaunchBlockedNotice.test.tsx
- LaunchBlockedNotice.tsx
- ParameterForm.test.tsx
- ParameterForm.tsx
- PerSampleValueGrid.test.tsx
- PerSampleValueGrid.tsx
- PipelineRunResultsTab.errors.test.tsx
- PipelineRunResultsTab.test.tsx
- PipelineRunResultsTab.tsx
- protocolDetection.test.ts
- protocolDetection.ts
- RegistryBrowseModal.tsx
- RegistryInstallAction.tsx
- RegistryUnreleased.test.tsx
- RunSamplesheetProvenance.test.tsx
- RunSamplesheetProvenance.tsx
- SamplesheetColumnEditor.test.tsx
- SamplesheetColumnEditor.tsx
- SamplesheetInputs.test.tsx
- SamplesheetInputs.tsx
- SamplesheetReview.test.tsx
- SamplesheetReview.tsx
- PlotThumbnail.test.tsx
- PlotThumbnail.tsx
- ProjectExportModal.tsx
- ProvenanceDAG.tsx
- ProvenanceReportPanel.tsx
- ChartSection.tsx
- format.ts
- GenericQCDashboard.tsx
- MetricCard.tsx
- MetricSection.tsx
- QCAiReviewSection.test.tsx
- QCAiReviewSection.tsx
- QCDashboardListItem.test.tsx
- QCDashboardListItem.tsx
- QCReportModal.test.tsx
- QCReportModal.tsx
- QualityBadge.tsx
- ReferencePicker.test.tsx
- ReferencePicker.tsx
- ReferenceStatusBadge.tsx
- referenceVersioning.test.ts
- referenceVersioning.ts
- UploadReferenceForm.test.tsx
- UploadReferenceForm.tsx
- UrlImportReferenceForm.test.tsx
- UrlImportReferenceForm.tsx
- AutoLitReviewSection.test.tsx
- AwsSettingsContent.test.tsx
- AwsSettingsContent.tsx
- GcpSettingsContent.test.tsx
- GcpSettingsContent.tsx
- LlmSettingsContent.test.tsx
- LlmSettingsContent.tsx
- NetworkingSettingsContent.tsx
- RoleEditorModal.tsx
- SheetsReaderSACard.tsx
- SlackSettingsContent.tsx
- SmtpSettingsContent.test.tsx
- SmtpSettingsContent.tsx
- AssaySelect.test.tsx
- AssaySelect.tsx
- ConfirmDialog.test.tsx
- ConfirmDialog.tsx
- ConnectButton.tsx
- ContentLoading.test.tsx
- ContentLoading.tsx
- DetailModal.tsx
- ErrorState.tsx
- ExportPdfButton.tsx
- ExtensibleVocabularySelect.tsx
- InputDialog.test.tsx
- InputDialog.tsx
- LoadingSpinner.test.tsx
- LoadingSpinner.tsx
- Modal.test.tsx
- Modal.tsx
- NotSet.test.tsx
- NotSet.tsx
- PageSizeSelect.test.tsx
- PageSizeSelect.tsx
- PlotModal.test.tsx
- PlotModal.tsx
- ProvenanceExportMenu.tsx
- QCCharts.tsx
- SessionBucketFilter.tsx
- StatusBadge.tsx
- Toast.test.tsx
- Toast.tsx
- VocabularySelect.tsx
- ThemeProvider.tsx
- ThemeToggle.test.tsx
- ThemeToggle.tsx
- Button.test.tsx
- Button.tsx
- Card.test.tsx
- Card.tsx
- DepositConflictNotice.test.tsx
- DepositConflictNotice.tsx
- Level3Gate.test.tsx
- Level3Gate.tsx
- Level3ResultPanel.test.tsx
- Level3ResultPanel.tsx
- LitValidationGate.test.tsx
- LitValidationGate.tsx
- PipelineInstallNotice.test.tsx
- PipelineInstallNotice.tsx
- RetryNotice.test.tsx
- RetryNotice.tsx
- SampleManifestPicker.tsx
- SamplesMismatchNotice.test.tsx
- SamplesMismatchNotice.tsx
- ValidatePaperButton.tsx
- ValidationEvidenceTable.tsx
- ValidationStatusBadge.test.tsx
- ValidationStatusBadge.tsx
- ValidationStudyActions.test.tsx
- ValidationStudyActions.tsx
- ValidationStudyOutcome.tsx
- ValidationVerdictPanel.tsx
- SnapshotComparison.tsx
- SnapshotComparisonTable.tsx
- SnapshotTimeline.tsx
- capabilitiesCache.ts
- permissionsCache.ts
- useBackendReady.test.ts
- useBackendReady.ts
- useBetaFeatures.ts
- useCapabilities.test.ts
- useCapabilities.ts
- useComponents.test.ts
- useComponents.ts
- useConfirm.test.tsx
- useConfirm.tsx
- useContentUrl.ts
- useDebouncedValue.test.ts
- useDebouncedValue.ts
- useDeploymentProgress.ts
- useDismissOnEscape.test.tsx
- useDismissOnEscape.ts
- useFocusTrap.test.tsx
- useFocusTrap.ts
- usePermissions.test.ts
- usePermissions.ts
- useStackOptions.test.ts
- useStackOptions.ts
- useVisibleNavSections.test.tsx
- useVisibleNavSections.ts
- useVocabulary.ts
- useWidgetData.test.tsx
- useWidgetData.ts
- a11y.test.ts
- a11y.ts
- api.test.ts
- api.ts
- auth.ts
- aws-regions.ts
- clusterMachineOptions.ts
- customPipelineVersions.ts
- errorReporting.test.ts
- errorReporting.ts
- experimentTabs.test.ts
- experimentTabs.ts
- fileNaming.ts
- gcp-regions.ts
- infrastructure.ts
- integrationsApi.ts
- labDocuments.ts
- literature.test.ts
- literature.ts
- navConfig.test.ts
- navConfig.ts
- notebookCapacity.ts
- notificationLinks.test.ts
- notificationLinks.ts
- pageTitle.test.ts
- pageTitle.ts
- pdfSecurity.ts
- placeholders.ts
- resumableUpload.test.ts
- resumableUpload.ts
- searchLinks.test.ts
- searchLinks.ts
- sessionRecreate.ts
- sessionStatus.ts
- statusStyles.test.ts
- statusStyles.ts
- storageDisplay.test.ts
- storageDisplay.ts
- theme.test.ts
- theme.ts
- types.ts
- validationClassification.test.ts
- validationClassification.ts
- validationStage.ts
- validationStatus.test.ts
- validationStatus.ts
- workNodeProfiles.test.ts
- workNodeProfiles.ts
- renderWithProviders.tsx
- upload.test.tsx
- list.test.tsx
- page.test.tsx
- InviteForm.test.tsx
- LoginForm.test.tsx
- SetupWizard.test.tsx
- SetupWizardAws.test.tsx
- ComponentPicker.test.tsx
- StorageSection.test.tsx
- widgets.test.tsx
- ExperimentStatusBadge.test.tsx
- GeoExportModal.test.tsx
- ReviewBadge.test.tsx
- ReviewPanel.test.tsx
- AutoIngestControls.test.tsx
- BootstrapCard.test.tsx
- ComponentsPage.test.tsx
- StorageSection.test.tsx
- TerraformPlanViewer.test.tsx
- TerraformProgressModal.test.tsx
- TerraformRunHistory.test.tsx
- Breadcrumb.test.tsx
- GcpNavItem.test.tsx
- Sidebar.test.tsx
- BranchConflictWarning.test.tsx
- NotificationBell.test.tsx
- NotificationItem.test.tsx
- ConnectButton.test.tsx
- ProvenanceExportMenu.test.tsx
- StatusBadge.test.tsx
- UIStates.test.tsx
- VocabularySelect.test.tsx
- SnapshotComparisonTable.test.tsx
- SnapshotTimeline.test.tsx
- ValidatePaperButton.test.tsx
- ValidationEvidenceTable.test.tsx
- ValidationStatusBadge.test.tsx
- ValidationStudyActions.test.tsx
- ValidationStudyOutcome.test.tsx
- ValidationVerdictPanel.test.tsx
- SessionBucketFilter.test.tsx
- appShellScroll.test.ts
- brandColor.test.ts
- clusterMachineOptions.test.ts
- notebookCapacity.test.ts
- sessionRecreate.test.ts
- sessionStatus.test.ts
- validationStage.test.ts
- validationStatus.test.ts
- activity.test.tsx
- dashboard-gcp-banner.test.tsx
- DataBrowser.test.tsx
- experiment-files-tab.test.tsx
- experiment-results-tab.test.tsx
- notebooks.test.tsx
- pipeline-runs-list.test.tsx
- pipeline-runs.test.tsx
- plot-archive.test.tsx
- settings-gcp.test.tsx
- settings-info.test.tsx
- settings-networking.test.tsx
- settings-workbench.test.tsx
- redirects.test.ts
- .eslintrc.json
- jest.config.js
- jest.setup.ts
- next-env.d.ts
- next.config.js
- package-lock.json
- package.json
- postcss.config.js
- tailwind.config.js
- tailwind.tokens.js
- tsconfig.json
- configmap.yaml
- cronjob-config-backup.yaml
- cronjob-db-backup.yaml
- deployment-backend.yaml
- deployment-frontend.yaml
- hpa.yaml
- ingress.yaml
- secret-encryption.yaml
- service-backend.yaml
- service-frontend.yaml
- serviceaccount.yaml
- Chart.yaml
- values.yaml
- output.sh
- quota.sh
- roles_manifest.yaml
- setup_audit_roles.sql
- bioaf-scrna.yml
- r-bioaf.R
- 01_qc_filtering.ipynb
- 02_normalization_dimreduction.ipynb
- 03_clustering_markers.ipynb
- 04_differential_expression.ipynb
- 05_trajectory_inference.ipynb
- de_pseudobulk_deseq2.ipynb
- bioaf-system-test.json
- nf-core-fetchngs.json
- nf-core-rnaseq.json
- nf-core-scrnaseq.json
- config.yaml
- nextflow.config.tpl
- cgroup.conf.tpl
- compute-startup.sh.tpl
- controller-startup.sh.tpl
- login-startup.sh.tpl
- slurm.conf.tpl
- build-scrna-image.sh
- update-agent.sh
- __init__.py
- anndata.py
- __init__.py
- client.py
- snapshot.py
- upload.py
- conftest.py
- test_anndata_extractor.py
- test_client.py
- test_snapshot.py
- pyproject.toml
- bioaf_connect.Rd
- bioaf_snapshot.Rd
- connect.R
- extractors.R
- snapshot.R
- upload.R
- test-connect.R
- test-extractors.R
- test-snapshot.R
- testthat.R
- DESCRIPTION
- NAMESPACE
- example_scrna_workflow.py
- test_bioaf.bats
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- .env.example
- .gitignore
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- CLAUDE.md
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- LICENSE
- README.md
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