BugSeq 0.1.0¶

Servers¶

Description	URL
https://api.bugseq.com	https://api.bugseq.com

users¶

GET /v1/users/me¶

Get Current User

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token

Responses

200 OK

application/json

{
    "id": "string",
    "email": "string",
    "first_name": "string",
    "last_name": "string",
    "created": "2022-04-13T15:42:05.901Z",
    "affiliation": "string",
    "billing_account_id": "string",
    "pipeline_version": null,
    "pinned_region": null,
    "enabled_features": [
        "string"
    ]
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the response body

{
    "properties": {
        "id": {
            "type": "string",
            "title": "Id"
        },
        "email": {
            "type": "string",
            "title": "Email"
        },
        "first_name": {
            "type": "string",
            "title": "First Name"
        },
        "last_name": {
            "type": "string",
            "title": "Last Name"
        },
        "created": {
            "type": "string",
            "format": "date-time",
            "title": "Created"
        },
        "affiliation": {
            "type": "string",
            "title": "Affiliation"
        },
        "billing_account_id": {
            "type": "string",
            "title": "Billing Account Id"
        },
        "pipeline_version": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "Pipeline Version"
        },
        "pinned_region": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "Pinned Region"
        },
        "enabled_features": {
            "items": {
                "type": "string"
            },
            "type": "array",
            "title": "Enabled Features"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "id",
        "email",
        "first_name",
        "last_name",
        "created",
        "affiliation",
        "billing_account_id",
        "enabled_features"
    ],
    "title": "UserResponse"
}

files¶

POST /v1/files/singlepart/init¶

Initialize Single Part Upload

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token

Request body

application/json

{
    "filename": "string",
    "s3_region": null,
    "skip_filename_validation": true
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the request body

{
    "properties": {
        "filename": {
            "type": "string",
            "title": "Filename"
        },
        "s3_region": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "S3 Region"
        },
        "skip_filename_validation": {
            "type": "boolean",
            "title": "Skip Filename Validation",
            "default": false
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "filename"
    ],
    "title": "FileCreateS3Request"
}

Responses

200 OK

application/json

{
    "id": "string",
    "presigned_s3_data": {
        "url": "string",
        "fields": {}
    }
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the response body

{
    "properties": {
        "id": {
            "type": "string",
            "title": "Id"
        },
        "presigned_s3_data": {
            "$ref": "#/components/schemas/PresignedPostData"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "id",
        "presigned_s3_data"
    ],
    "title": "FileInitSinglepartUploadS3Response"
}

POST /v1/files/multipart/init¶

Initialize Multipart Upload

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token

Request body

application/json

{
    "filename": "string",
    "s3_region": null,
    "skip_filename_validation": true
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the request body

{
    "properties": {
        "filename": {
            "type": "string",
            "title": "Filename"
        },
        "s3_region": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "S3 Region"
        },
        "skip_filename_validation": {
            "type": "boolean",
            "title": "Skip Filename Validation",
            "default": false
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "filename"
    ],
    "title": "FileCreateS3Request"
}

Responses

200 OK

application/json

{
    "id": "string",
    "presigned_s3_data": {
        "UploadId": "string"
    }
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the response body

{
    "properties": {
        "id": {
            "type": "string",
            "title": "Id"
        },
        "presigned_s3_data": {
            "$ref": "#/components/schemas/MultipartUploadInit"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "id",
        "presigned_s3_data"
    ],
    "title": "FileInitMultipartUploadS3Response"
}

POST /v1/files/multipart/chunk¶

Presign Multipart Chunk

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token

Request body

application/json

{
    "file_id": "string",
    "upload_id": "string",
    "part_number": 0
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the request body

{
    "properties": {
        "file_id": {
            "type": "string",
            "title": "File Id"
        },
        "upload_id": {
            "type": "string",
            "title": "Upload Id"
        },
        "part_number": {
            "type": "integer",
            "title": "Part Number"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "file_id",
        "upload_id",
        "part_number"
    ],
    "title": "FileMultipartChunkInitUploadRequest"
}

Responses

200 OK

application/json

{
    "id": "string",
    "presigned_s3_data": "string"
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the response body

{
    "properties": {
        "id": {
            "type": "string",
            "title": "Id"
        },
        "presigned_s3_data": {
            "type": "string",
            "title": "Presigned S3 Data"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "id",
        "presigned_s3_data"
    ],
    "title": "FileMultipartChunkInitUploadResponse"
}

POST /v1/files/multipart/complete¶

Complete Multipart Upload

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token

Request body

application/json

{
    "file_id": "string",
    "upload_id": "string",
    "parts": [
        {
            "ETag": "string",
            "PartNumber": 0
        }
    ]
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the request body

{
    "properties": {
        "file_id": {
            "type": "string",
            "title": "File Id"
        },
        "upload_id": {
            "type": "string",
            "title": "Upload Id"
        },
        "parts": {
            "items": {
                "$ref": "#/components/schemas/MultipartUploadPart"
            },
            "type": "array",
            "maxItems": 10000,
            "minItems": 1,
            "title": "Parts"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "file_id",
        "upload_id",
        "parts"
    ],
    "title": "FileMultipartUploadCompleteRequest"
}

Responses

200 OK

application/json

Schema of the response body

POST /v1/files/basespace/sample¶

Create Basespace File

Description

Register a BaseSpace biosample as a file. Its fastqs are pulled from BaseSpace when an analysis using it starts, so nothing is uploaded here.

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token

Request body

application/json

{
    "basespace_project_id": "string",
    "basespace_project_name": "string",
    "basespace_sample_id": "string",
    "basespace_sample_name": "string"
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the request body

{
    "properties": {
        "basespace_project_id": {
            "type": "string",
            "title": "Basespace Project Id"
        },
        "basespace_project_name": {
            "type": "string",
            "title": "Basespace Project Name"
        },
        "basespace_sample_id": {
            "type": "string",
            "title": "Basespace Sample Id"
        },
        "basespace_sample_name": {
            "type": "string",
            "title": "Basespace Sample Name"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "basespace_project_id",
        "basespace_project_name",
        "basespace_sample_id",
        "basespace_sample_name"
    ],
    "title": "FileCreateBasespaceRequest"
}

Responses

200 OK

application/json

{
    "id": "string",
    "created": "2022-04-13T15:42:05.901Z",
    "filename": null,
    "s3_region": null,
    "s3_bucket": null,
    "s3_key": null,
    "basespace_sample_id": null,
    "sra_accession": null
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the response body

{
    "properties": {
        "id": {
            "type": "string",
            "title": "Id"
        },
        "created": {
            "type": "string",
            "format": "date-time",
            "title": "Created"
        },
        "filename": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "Filename"
        },
        "s3_region": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "S3 Region"
        },
        "s3_bucket": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "S3 Bucket"
        },
        "s3_key": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "S3 Key"
        },
        "basespace_sample_id": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "Basespace Sample Id"
        },
        "sra_accession": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "Sra Accession"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "id",
        "created"
    ],
    "title": "FileResponse"
}

jobs¶

POST /v1/jobs/¶

Submit Analysis

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token

Request body

application/json

{
    "user_provided_name": null,
    "aws_region": null,
    "file_ids": [
        "string"
    ],
    "run_options": {
        "platform": "NANOPORE",
        "kit": null,
        "metagenomic_database": "BUGSEQ_DEFAULT",
        "sample_type": "ABSCESS",
        "molecule_type": "DNA",
        "include_in_lab_db": true,
        "filter_animal_reads": null
    },
    "lab_id": null,
    "testmode": true,
    "user_provided_metadata": null,
    "pipeline_version": null
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the request body

{
    "properties": {
        "user_provided_name": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "User Provided Name"
        },
        "aws_region": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "Aws Region"
        },
        "file_ids": {
            "items": {
                "type": "string"
            },
            "type": "array",
            "title": "File Ids"
        },
        "run_options": {
            "$ref": "#/components/schemas/RunOptions"
        },
        "lab_id": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "Lab Id"
        },
        "testmode": {
            "type": "boolean",
            "title": "Testmode",
            "default": false
        },
        "user_provided_metadata": {
            "anyOf": [
                {
                    "items": {
                        "additionalProperties": {
                            "anyOf": [
                                {
                                    "type": "boolean"
                                },
                                {
                                    "type": "string"
                                }
                            ]
                        },
                        "type": "object"
                    },
                    "type": "array"
                },
                {
                    "type": "null"
                }
            ],
            "title": "User Provided Metadata"
        },
        "pipeline_version": {
            "anyOf": [
                {
                    "$ref": "#/components/schemas/PipelineVersion"
                },
                {
                    "type": "null"
                }
            ]
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "file_ids",
        "run_options"
    ],
    "title": "JobRunSubmitRequest"
}

Responses

200 OK

application/json

{
    "id": "string"
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the response body

{
    "properties": {
        "id": {
            "type": "string",
            "title": "Id"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "id"
    ],
    "title": "JobRunSubmitResponse"
}

GET /v1/jobs/¶

List Analyses

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token
`ids`	query			No
`lab_ids`	query			No
`limit`	query	integer	20	No
`owner_ids`	query			No
`skip`	query	integer	0	No
`user_provided_name`	query			No

Responses

200 OK

application/json

{
    "job_runs": [
        {
            "id": "string",
            "user_provided_name": null,
            "owner_id": "string",
            "created": "2022-04-13T15:42:05.901Z",
            "end_time": null,
            "job_status": "created",
            "results_url": "string",
            "org_id": null,
            "pipeline_version": "latest"
        }
    ],
    "has_more": true
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the response body

{
    "properties": {
        "job_runs": {
            "items": {
                "$ref": "#/components/schemas/JobRunResponse"
            },
            "type": "array",
            "title": "Job Runs"
        },
        "has_more": {
            "type": "boolean",
            "title": "Has More"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "job_runs",
        "has_more"
    ],
    "title": "JobRunListResponse"
}

GET /v1/jobs/{job_id}/results¶

Get Analysis Results

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token
`job_id`	path	string		No

Responses

200 OK

application/json

{
    "id": "string",
    "user_provided_name": null,
    "owner_id": "string",
    "created": "2022-04-13T15:42:05.901Z",
    "end_time": null,
    "job_status": "created",
    "inputs": [
        {
            "filename": "string",
            "size": null
        }
    ],
    "outputs": null,
    "org_id": null,
    "pipeline_version": "latest"
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the response body

{
    "properties": {
        "id": {
            "type": "string",
            "title": "Id"
        },
        "user_provided_name": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "User Provided Name"
        },
        "owner_id": {
            "type": "string",
            "title": "Owner Id"
        },
        "created": {
            "type": "string",
            "format": "date-time",
            "title": "Created"
        },
        "end_time": {
            "anyOf": [
                {
                    "type": "string",
                    "format": "date-time"
                },
                {
                    "type": "null"
                }
            ],
            "title": "End Time"
        },
        "job_status": {
            "$ref": "#/components/schemas/JobStatus"
        },
        "inputs": {
            "items": {
                "$ref": "#/components/schemas/JobRunFileResponse"
            },
            "type": "array",
            "title": "Inputs"
        },
        "outputs": {
            "anyOf": [
                {
                    "items": {
                        "$ref": "#/components/schemas/JobRunFileResponse"
                    },
                    "type": "array"
                },
                {
                    "type": "null"
                }
            ],
            "title": "Outputs"
        },
        "org_id": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "Org Id"
        },
        "pipeline_version": {
            "$ref": "#/components/schemas/PipelineVersion"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "id",
        "owner_id",
        "created",
        "job_status",
        "inputs",
        "outputs",
        "org_id",
        "pipeline_version"
    ],
    "title": "JobRunResultsResponse"
}

GET /v1/jobs/{job_id}/results/download¶

Download Analysis Result

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token
`filename`	query	string		No
`job_id`	path	string		No

Responses

200 OK

application/json

{
    "url": "string"
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the response body

{
    "properties": {
        "url": {
            "type": "string",
            "title": "Url"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "url"
    ],
    "title": "FileDownloadResponse"
}

billing¶

GET /v1/billing/{billing_account_id}/credits/sample¶

List Billing Account Sample Credits

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token
`billing_account_id`	path	string		No
`include_expired`	query	boolean	True	No
`limit`	query	integer	20	No
`remaining_count_gt`	query			No
`skip`	query	integer	0	No
`sort_by`	query	string	expiration	No
`sort_dir`	query	string	asc	No

Responses

200 OK

application/json

{
    "items": [
        {
            "id": "string",
            "sample_type": "metagenomic",
            "initial_count": 0,
            "remaining_count": 0,
            "expiration": "2022-04-13T15:42:05.901Z",
            "billing_account_id": "string",
            "created": "2022-04-13T15:42:05.901Z",
            "is_signup_trial_credit": true
        }
    ],
    "has_more": true
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the response body

{
    "properties": {
        "items": {
            "items": {
                "$ref": "#/components/schemas/BillingAccountSampleCreditResponse"
            },
            "type": "array",
            "title": "Items"
        },
        "has_more": {
            "type": "boolean",
            "title": "Has More"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "items",
        "has_more"
    ],
    "title": "ListBillingAccountSampleCreditResponse"
}

basespace¶

GET /v1/basespace/runs/for-sequencing-run/{sequencing_run_id}¶

Run For Sequencing Run

Description

Look up the run with an srn. sequencing run id – the id the instrument’s cloud assigns, and the only id an Illumina event names a run by. BaseSpace cannot query it, so it is matched by scanning recent runs.

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token
`sequencing_run_id`	path	string		No

Responses

200 OK

application/json

{
    "run_id": "string",
    "run_name": "string",
    "experiment_name": null,
    "sequencing_run_id": null,
    "status": "string"
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the response body

{
    "properties": {
        "run_id": {
            "type": "string",
            "title": "Run Id"
        },
        "run_name": {
            "type": "string",
            "title": "Run Name"
        },
        "experiment_name": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "Experiment Name"
        },
        "sequencing_run_id": {
            "anyOf": [
                {
                    "type": "string"
                },
                {
                    "type": "null"
                }
            ],
            "title": "Sequencing Run Id"
        },
        "status": {
            "type": "string",
            "title": "Status"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "run_id",
        "run_name",
        "experiment_name",
        "sequencing_run_id",
        "status"
    ],
    "title": "BasespaceRun"
}

GET /v1/basespace/runs/{run_id}/samples¶

Run Samples

Description

List the biosamples on a run that have fastqs to pull, so a whole run can be submitted as one analysis. Returns 409 while any biosample planned for the run is still missing its fastqs, which callers should treat as retryable.

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token
`run_id`	path	string		No

Responses

200 OK

application/json

{
    "run_id": "string",
    "run_name": "string",
    "items": [
        {
            "basespace_sample_id": "string",
            "basespace_sample_name": "string",
            "basespace_project_id": "string",
            "basespace_project_name": "string"
        }
    ]
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the response body

{
    "properties": {
        "run_id": {
            "type": "string",
            "title": "Run Id"
        },
        "run_name": {
            "type": "string",
            "title": "Run Name"
        },
        "items": {
            "items": {
                "$ref": "#/components/schemas/BasespaceRunSample"
            },
            "type": "array",
            "title": "Items"
        }
    },
    "additionalProperties": false,
    "type": "object",
    "required": [
        "run_id",
        "run_name",
        "items"
    ],
    "title": "ListBasespaceRunSamplesResponse"
}

organization¶

GET /v1/organization/membership¶

List Memberships

Input parameters

Parameter	In	Type	Default	Nullable	Description
`HTTPBearer`	header	string	N/A	No	JWT Bearer token
`limit`	query	integer	20	No
`role`	query			No
`skip`	query	integer	0	No

Responses

200 OK

application/json

{
    "items": [
        {
            "id": "string",
            "name": "string",
            "manager_id": "string",
            "auto_share_analyses": true,
            "members_retain_billing_account": true,
            "metadata_keys": [
                "string"
            ],
            "created": "2022-04-13T15:42:05.901Z",
            "percent_identity_to_reference_genome_threshold": null,
            "median_coverage_of_reference_genome_threshold": null,
            "assembly_completeness_threshold": null,
            "assembly_duplication_threshold": null,
            "number_of_contigs_warn_threshold": null,
            "number_of_contigs_fail_threshold": null,
            "length_qc_tukeys_k_warn_threshold": null,
            "length_qc_tukeys_k_fail_threshold": null,
            "gc_content_qc_tukeys_k_warn_threshold": null,
            "gc_content_qc_tukeys_k_fail_threshold": null,
            "ambiguous_loci_percent_threshold": null,
            "default_outbreak_allele_cutoff": null,
            "per_taxid_outbreak_parameters": null,
            "per_sample_type_metagenomic_thresholds": null,
            "generate_ai_summary_in_reports": true,
            "default_molecule_type": null,
            "default_molecule_type_enforced": true,
            "default_platform": null,
            "default_platform_enforced": true,
            "default_kit": null,
            "default_kit_enforced": true,
            "default_metagenomic_database": null,
            "default_metagenomic_database_enforced": true,
            "default_sample_type": null,
            "default_sample_type_enforced": true,
            "default_pipeline_version": null,
            "force_experimental_design": "AUTODETECT",
            "default_breakpoint_standard": null,
            "is_ranger_lab": true,
            "member_preferences": {
                "emails_enabled_org_share": null,
                "is_default_for_submission": null
            },
            "members": [
                {
                    "id": "string",
                    "first_name": "string",
                    "last_name": "string",
                    "email": "string",
                    "member_role": "REVIEWER"
                }
            ]
        }
    ],
    "has_more": true
}

⚠️ This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.

Schema of the response body

{
    "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"
}

Schemas¶

app__db_models__billing_account_sample__SampleType¶

Type: string

appmodelsjob_run_options__SampleType¶

Type: string

BasespaceRun¶

Name	Type	Description
`experiment_name`
`run_id`	string
`run_name`	string
`sequencing_run_id`
`status`	string

BasespaceRunSample¶

Name	Type	Description
`basespace_project_id`	string
`basespace_project_name`	string
`basespace_sample_id`	string
`basespace_sample_name`	string

BillingAccountSampleCreditResponse¶

Name	Type	Description
`billing_account_id`	string
`created`	string(date-time)
`expiration`	string(date-time)
`id`	string
`initial_count`	integer
`is_signup_trial_credit`	boolean
`remaining_count`	integer
`sample_type`	app__db_models__billing_account_sample__SampleType

BreakpointStandard¶

Type: string

ExperimentalDesign¶

Type: string

FileCreateBasespaceRequest¶

Name	Type	Description
`basespace_project_id`	string
`basespace_project_name`	string
`basespace_sample_id`	string
`basespace_sample_name`	string

FileCreateS3Request¶

Name	Type	Description
`filename`	string
`s3_region`
`skip_filename_validation`	boolean

FileDownloadResponse¶

Name	Type	Description
`url`	string

FileInitMultipartUploadS3Response¶

Name	Type	Description
`id`	string
`presigned_s3_data`	MultipartUploadInit

FileInitSinglepartUploadS3Response¶

Name	Type	Description
`id`	string
`presigned_s3_data`	PresignedPostData

FileMultipartChunkInitUploadRequest¶

Name	Type	Description
`file_id`	string
`part_number`	integer
`upload_id`	string

FileMultipartChunkInitUploadResponse¶

Name	Type	Description
`id`	string
`presigned_s3_data`	string

FileMultipartUploadCompleteRequest¶

Name	Type	Description
`file_id`	string
`parts`	Array<MultipartUploadPart>
`upload_id`	string

FileResponse¶

Name	Type	Description
`basespace_sample_id`
`created`	string(date-time)
`filename`
`id`	string
`s3_bucket`
`s3_key`
`s3_region`
`sra_accession`

HTTPValidationError¶

Name	Type	Description
`detail`	Array<ValidationError>

JobRunFileResponse¶

Name	Type	Description
`filename`	string
`size`

JobRunListResponse¶

Name	Type	Description
`has_more`	boolean
`job_runs`	Array<JobRunResponse>

JobRunResponse¶

Name	Type	Description
`created`	string(date-time)
`end_time`
`id`	string
`job_status`	JobStatus
`org_id`
`owner_id`	string
`pipeline_version`	PipelineVersion
`results_url`	string
`user_provided_name`

JobRunResultsResponse¶

Name	Type	Description
`created`	string(date-time)
`end_time`
`id`	string
`inputs`	Array<JobRunFileResponse>
`job_status`	JobStatus
`org_id`
`outputs`
`owner_id`	string
`pipeline_version`	PipelineVersion
`user_provided_name`

JobRunSubmitRequest¶

Name	Type	Description
`aws_region`
`file_ids`	Array<string>
`lab_id`
`pipeline_version`
`run_options`	RunOptions
`testmode`	boolean
`user_provided_metadata`
`user_provided_name`

JobRunSubmitResponse¶

Name	Type	Description
`id`	string

JobStatus¶

Type: string

Kit¶

Type: string

ListBasespaceRunSamplesResponse¶

Name	Type	Description
`items`	Array<BasespaceRunSample>
`run_id`	string
`run_name`	string

ListBillingAccountSampleCreditResponse¶

Name	Type	Description
`has_more`	boolean
`items`	Array<BillingAccountSampleCreditResponse>

ListMembershipsItemResponse¶

Name	Type	Description
`ambiguous_loci_percent_threshold`
`assembly_completeness_threshold`
`assembly_duplication_threshold`
`auto_share_analyses`	boolean
`created`	string(date-time)
`default_breakpoint_standard`
`default_kit`
`default_kit_enforced`	boolean
`default_metagenomic_database`
`default_metagenomic_database_enforced`	boolean
`default_molecule_type`
`default_molecule_type_enforced`	boolean
`default_outbreak_allele_cutoff`
`default_pipeline_version`
`default_platform`
`default_platform_enforced`	boolean
`default_sample_type`
`default_sample_type_enforced`	boolean
`force_experimental_design`	ExperimentalDesign
`gc_content_qc_tukeys_k_fail_threshold`
`gc_content_qc_tukeys_k_warn_threshold`
`generate_ai_summary_in_reports`	boolean
`id`	string
`is_ranger_lab`	boolean
`length_qc_tukeys_k_fail_threshold`
`length_qc_tukeys_k_warn_threshold`
`manager_id`	string
`median_coverage_of_reference_genome_threshold`
`member_preferences`	OrganizationMembershipPreferencesResponse
`members`	Array<OrganizationMemberResponse>
`members_retain_billing_account`	boolean
`metadata_keys`	Array<string>
`name`	string
`number_of_contigs_fail_threshold`
`number_of_contigs_warn_threshold`
`per_sample_type_metagenomic_thresholds`
`per_taxid_outbreak_parameters`
`percent_identity_to_reference_genome_threshold`

ListMembershipsResponse¶

Name	Type	Description
`has_more`	boolean
`items`	Array<ListMembershipsItemResponse>

MetagenomicDatabase¶

Type: string

MetagenomicDetectionThresholdParameters¶

Name	Type	Description
`horizontal_genome_coverage_gt_1x`
`median_alignment_length`
`median_percent_read_aligned`
`negative_control_multiplicity_summed`
`pathogen_ordering_priorities`
`pathogen_prioritization_specifications`
`read_count_at_rank`
`read_count_summed`
`relative_abundance`
`unique_read_alignments`

MoleculeType¶

Type: string

MultipartUploadInit¶

Name	Type	Description
`UploadId`	string

MultipartUploadPart¶

Name	Type	Description
`ETag`	string
`PartNumber`	integer

OrganizationMemberResponse¶

Name	Type	Description
`email`	string
`first_name`	string
`id`	string
`last_name`	string
`member_role`	OrgMemberRole

OrganizationMembershipPreferencesResponse¶

Name	Type	Description
`emails_enabled_org_share`
`is_default_for_submission`

OrgMemberRole¶

Type: string

OutbreakAlleleCutoff¶

Type: string

PathogenicityClassification¶

Type: string

PathogenicityDisplayCategory¶

Type: string

PathogenicityTaxaEntry¶

Name	Type	Description
`species_name`	string
`species_taxid`	integer

PerSampleTypeMetagenomicThresholds¶

PerTaxidOutbreakParameters¶

Name	Type	Description
`new_sample_alert_cutoff`	OutbreakAlleleCutoff
`species_name`	string
`species_taxid`	integer

PipelineVersion¶

Type: string

Platform¶

Type: string

PresignedPostData¶

Name	Type	Description
`fields`
`url`	string

RunOptions¶

Name	Type	Description
`filter_animal_reads`
`include_in_lab_db`	boolean
`kit`
`metagenomic_database`	MetagenomicDatabase
`molecule_type`	MoleculeType
`platform`	Platform
`sample_type`	SampleType-Input

SampleType-Input¶

Type: string

UserResponse¶

Name	Type	Description
`affiliation`	string
`billing_account_id`	string
`created`	string(date-time)
`email`	string
`enabled_features`	Array<string>
`first_name`	string
`id`	string
`last_name`	string
`pinned_region`
`pipeline_version`

ValidationError¶

Name	Type	Description
`ctx`
`input`
`loc`	Array<>
`msg`	string
`type`	string

Security schemes¶

Name	Type	Scheme	Description
HTTPBearer	http	bearer

BugSeq 0.1.0¶

Servers¶

users¶

GET /v1/users/me¶

files¶

POST /v1/files/singlepart/init¶

POST /v1/files/multipart/init¶

POST /v1/files/multipart/chunk¶

POST /v1/files/multipart/complete¶

POST /v1/files/basespace/sample¶

jobs¶

POST /v1/jobs/¶

GET /v1/jobs/¶

GET /v1/jobs/{job_id}/results¶

GET /v1/jobs/{job_id}/results/download¶

billing¶

GET /v1/billing/{billing_account_id}/credits/sample¶

basespace¶

GET /v1/basespace/runs/for-sequencing-run/{sequencing_run_id}¶

GET /v1/basespace/runs/{run_id}/samples¶

organization¶

GET /v1/organization/membership¶

Schemas¶

app__db_models__billing_account_sample__SampleType¶

app__models__job_run_options__SampleType¶

BasespaceRun¶

BasespaceRunSample¶

BillingAccountSampleCreditResponse¶

BreakpointStandard¶

ExperimentalDesign¶

FileCreateBasespaceRequest¶

FileCreateS3Request¶

FileDownloadResponse¶

FileInitMultipartUploadS3Response¶

FileInitSinglepartUploadS3Response¶

FileMultipartChunkInitUploadRequest¶

FileMultipartChunkInitUploadResponse¶

FileMultipartUploadCompleteRequest¶

FileResponse¶

HTTPValidationError¶

JobRunFileResponse¶

JobRunListResponse¶

JobRunResponse¶

JobRunResultsResponse¶

JobRunSubmitRequest¶

JobRunSubmitResponse¶

JobStatus¶

Kit¶

ListBasespaceRunSamplesResponse¶

ListBillingAccountSampleCreditResponse¶

ListMembershipsItemResponse¶

ListMembershipsResponse¶

MetagenomicDatabase¶

MetagenomicDetectionThresholdParameters¶

MoleculeType¶

MultipartUploadInit¶

MultipartUploadPart¶

OrganizationMemberResponse¶

OrganizationMembershipPreferencesResponse¶

OrgMemberRole¶

OutbreakAlleleCutoff¶

PathogenicityClassification¶

PathogenicityDisplayCategory¶

PathogenicityTaxaEntry¶

PerSampleTypeMetagenomicThresholds¶

PerTaxidOutbreakParameters¶

PipelineVersion¶

Platform¶

PresignedPostData¶

RunOptions¶

SampleType-Input¶

UserResponse¶

ValidationError¶

Security schemes¶

appmodelsjob_run_options__SampleType¶