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"title": "Testmode", "default": false }, "user_provided_metadata": { "anyOf": [ { "items": { "additionalProperties": { "anyOf": [ { "type": "boolean" }, { "type": "string" } ] }, "type": "object" }, "type": "array" }, { "type": "null" } ], "title": "User Provided Metadata" }, "pipeline_version": { "anyOf": [ { "$ref": "#/components/schemas/PipelineVersion" }, { "type": "null" } ] } }, "additionalProperties": false, "type": "object", "required": [ "file_ids", "run_options" ], "title": "JobRunSubmitRequest" }, "JobRunSubmitResponse": { "properties": { "id": { "type": "string", "title": "Id" } }, "additionalProperties": false, "type": "object", "required": [ "id" ], "title": "JobRunSubmitResponse" }, "JobStatus": { "type": "string", "enum": [ "created", "pending", "running", "success", "failure", "marked_in_error" ], "title": "JobStatus" }, "Kit": { "type": "string", "enum": [ "MINION_R9_4_1", "MINION_R10_3", "MINION_Q20", "PROMETHION_R9_4_1", "PROMETHION_Q20", "MINION_R10_4_1", 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"type": "null" } ], "title": "Percent Identity To Reference Genome Threshold" }, "median_coverage_of_reference_genome_threshold": { "anyOf": [ { "type": "integer" }, { "type": "null" } ], "title": "Median Coverage Of Reference Genome Threshold" }, "assembly_completeness_threshold": { "anyOf": [ { "type": "integer" }, { "type": "null" } ], "title": "Assembly Completeness Threshold" }, "assembly_duplication_threshold": { "anyOf": [ { "type": "integer" }, { "type": "null" } ], "title": "Assembly Duplication Threshold" }, "number_of_contigs_warn_threshold": { "anyOf": [ { "type": "integer" }, { "type": "null" } ], "title": "Number Of Contigs Warn Threshold" }, "number_of_contigs_fail_threshold": { "anyOf": [ { "type": "integer" }, { "type": "null" } ], "title": "Number Of Contigs Fail Threshold" }, "length_qc_tukeys_k_warn_threshold": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "title": "Length Qc Tukeys K Warn Threshold" }, "length_qc_tukeys_k_fail_threshold": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "title": "Length Qc Tukeys K Fail Threshold" }, "gc_content_qc_tukeys_k_warn_threshold": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "title": "Gc Content Qc Tukeys K Warn Threshold" }, "gc_content_qc_tukeys_k_fail_threshold": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "title": "Gc Content Qc Tukeys K Fail Threshold" }, "default_outbreak_allele_cutoff": { "anyOf": [ { "$ref": "#/components/schemas/OutbreakAlleleCutoff" }, { "type": "null" } ] }, "per_taxid_outbreak_parameters": { "anyOf": [ { "items": { "$ref": "#/components/schemas/PerTaxidOutbreakParameters" }, "type": "array" }, { "type": "null" } ], "title": "Per Taxid Outbreak Parameters" }, "per_sample_type_metagenomic_thresholds": { "anyOf": [ { "$ref": "#/components/schemas/PerSampleTypeMetagenomicThresholds" }, { "type": "null" } ] }, "generate_ai_summary_in_reports": { "type": "boolean", "title": "Generate Ai Summary In Reports" }, "default_molecule_type": { "anyOf": [ { "$ref": "#/components/schemas/MoleculeType" }, { "type": "null" } ] }, "default_molecule_type_enforced": { "type": "boolean", "title": "Default Molecule Type Enforced" }, "default_platform": { "anyOf": [ { "$ref": "#/components/schemas/Platform" }, { "type": "null" } ] }, "default_platform_enforced": { "type": "boolean", "title": "Default Platform Enforced" }, "default_kit": { "anyOf": [ { "$ref": "#/components/schemas/Kit" }, { "type": "null" } ] }, "default_kit_enforced": { "type": "boolean", "title": "Default Kit Enforced" }, "default_metagenomic_database": { "anyOf": [ { "$ref": "#/components/schemas/MetagenomicDatabase" }, { "type": "null" } ] }, "default_metagenomic_database_enforced": { "type": "boolean", "title": "Default Metagenomic Database Enforced" }, "default_sample_type": { "anyOf": [ { "$ref": "#/components/schemas/app__models__job_run_options__SampleType" }, { "type": "null" } ] }, "default_sample_type_enforced": { "type": "boolean", "title": "Default Sample Type Enforced" }, "default_pipeline_version": { "anyOf": [ { "$ref": "#/components/schemas/PipelineVersion" }, { "type": "null" } ] }, "force_experimental_design": { "$ref": "#/components/schemas/ExperimentalDesign" }, "default_breakpoint_standard": { "anyOf": [ { "$ref": "#/components/schemas/BreakpointStandard" }, { "type": "null" } ] }, "member_preferences": { "$ref": "#/components/schemas/OrganizationMembershipPreferencesResponse" }, "members": { "items": { "$ref": "#/components/schemas/OrganizationMemberResponse" }, "type": "array", "title": "Members" } }, "additionalProperties": false, "type": "object", "required": [ "id", "name", "manager_id", "auto_share_analyses", "metadata_keys", "created", "percent_identity_to_reference_genome_threshold", "median_coverage_of_reference_genome_threshold", "assembly_completeness_threshold", "assembly_duplication_threshold", "number_of_contigs_warn_threshold", "number_of_contigs_fail_threshold", "length_qc_tukeys_k_warn_threshold", "length_qc_tukeys_k_fail_threshold", "gc_content_qc_tukeys_k_warn_threshold", "gc_content_qc_tukeys_k_fail_threshold", "default_outbreak_allele_cutoff", "per_taxid_outbreak_parameters", "per_sample_type_metagenomic_thresholds", "generate_ai_summary_in_reports", "default_molecule_type", "default_molecule_type_enforced", "default_platform", "default_platform_enforced", "default_kit", "default_kit_enforced", "default_metagenomic_database", "default_metagenomic_database_enforced", "default_sample_type", "default_sample_type_enforced", "default_pipeline_version", "force_experimental_design", "default_breakpoint_standard", "member_preferences", "members" ], "title": "ListMembershipsItemResponse" }, "ListMembershipsResponse": { "properties": { "items": { "items": { "$ref": "#/components/schemas/ListMembershipsItemResponse" }, "type": "array", "title": "Items" }, "has_more": { "type": "boolean", "title": "Has More" } }, "additionalProperties": false, "type": "object", "required": [ "items", "has_more" ], "title": "ListMembershipsResponse" }, "MetagenomicDatabase": { "type": "string", "enum": [ "BUGSEQ_DEFAULT", "NCBI_NT" ], "title": "MetagenomicDatabase" }, "MetagenomicDetectionThresholdParameters": { "properties": { "unique_read_alignments": { "anyOf": [ { "type": "integer" }, { "type": "null" } ], "title": "Unique Read Alignments" }, "read_count_summed": { "anyOf": [ { "type": "integer" }, { "type": "null" } ], "title": "Read Count Summed" }, "read_count_at_rank": { "anyOf": [ { "type": "integer" }, { "type": "null" } ], "title": "Read Count At Rank" }, "negative_control_multiplicity_summed": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "title": "Negative Control Multiplicity Summed" }, "relative_abundance": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "title": "Relative Abundance" }, "horizontal_genome_coverage_gt_1x": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "title": "Horizontal Genome Coverage Gt 1X" }, 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