ReferenceFile
Summary of SMaHT Portal object type ReferenceFile . Its parent type is: File. Property names in red are required properties; those in blue are identifying properties; and properties with types in green are reference properties.Description: Reference file for bioinformatics pipelines.
Tip
See actual ReferenceFile data hereRequired Properties
| Property | Type | Description |
|---|---|---|
| data_category | array of enum | See below for more details. |
| data_type | array of enum | See below for more details. |
| file_format | FileFormat string | See below for more details. See values here |
| At least one of the following ... | ||
| consortia | Consortium array of string | See below for more details. See values here |
| submission_centers | SubmissionCenter array of string | See below for more details. See values here |
Identifying Properties
| Property | Type | Description |
|---|---|---|
| accession | string | See below for more details. |
| aliases | array of string | See below for more details. |
| uuid | string | See below for more details. |
Reference Properties
| Property | Type | Description |
|---|---|---|
| consortia | Consortium array of string | See below for more details. See values here |
| file_format | FileFormat string | See below for more details. See values here |
| meta_workflow_run_inputs | MetaWorkflowRun array of string | See below for more details. |
| meta_workflow_run_outputs | MetaWorkflowRun array of string | See below for more details. |
| quality_metrics | QualityMetric array of string | See below for more details. |
| sequencing_center | SubmissionCenter string | See below for more details. See values here |
| submission_centers | SubmissionCenter array of string | See below for more details. See values here |
Properties
| Property | Type | Description |
|---|---|---|
| accession | string | A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.] |
| aliases | array of string • unique • restricted | Institution-specific ID (e.g. bgm:cohort-1234-a). Must adhere to (regex) pattern: ^[^\s\\\/]+:[^\s\\\/]+$ |
| alternate_accessions | array of string • restricted | Accessions previously assigned to objects that have been merged with this object. [Only admins are allowed to set or update this value.] |
| consortia | Consortium • array of string • unique • restricted | Consortia associated with this item. See values here |
| content_md5sum | string • format: hex | The MD5 checksum of the uncompressed file. |
| data_category • Genome Region • Germline Variant Calls • Quality Control • Reference Genome • Sequencing Reads • Somatic Variant Calls | array of enum • min items: 1 • unique | Category for information in the file. |
| data_type • Aligned Reads • CNV • Image • Indel • Index • MEI • Reference Sequence • SNV • SV • Sequence Interval • Statistics • Unaligned Reads | array of enum • min items: 1 • unique | - |
| description | string | Plain text description of the item. |
| display_title | string • calculated | A calculated title for every object. |
| extra_files | array of object • min items: 1 • restricted | Links to extra files on s3 that don't have associated metadata. |
| extra_files . file_format | FileFormat • string | See values here |
| extra_files . file_size | integer | - |
| extra_files . filename | string | - |
| extra_files . href | string | - |
| extra_files . md5sum | string • format: hex | - |
| extra_files . status • archived • current • deleted • in review • inactive • obsolete • replaced • shared • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| file_access_status • Open • Protected | enum of string • calculated | Access status for the file contents. |
| file_format | FileFormat • string | See values here |
| file_size | integer | Size of file on disk. |
| filename | string | The local file name used at time of submission. Must be alphanumeric, with the exception of the following special characters: '+=,.@-_'. Must adhere to (regex) pattern: ^[\w+=,.@-]*$ |
| href | string • calculated | Use this link to download this file. |
| md5sum | string • format: hex | The MD5 checksum of the file being transferred. |
| meta_workflow_run_inputs | MetaWorkflowRun • array of string • calculated | - |
| meta_workflow_run_outputs | MetaWorkflowRun • array of string • calculated | - |
| o2_path | string | Path to file on O2. |
| quality_metrics | QualityMetric • array of string • min items: 1 • unique • restricted | Associated QC reports. |
| s3_lifecycle_category • ignore • long_term_access • long_term_access_long_term_archive • long_term_archive • no_storage • short_term_access • short_term_access_long_term_archive • short_term_archive | enum of string | The lifecycle category determines how long a file remains in a certain storage class. If set to ignore, lifecycle management will have no effect on this file. |
| s3_lifecycle_last_checked | string • format: date | date-time | Date when the lifecycle status of the file was last checked. |
| s3_lifecycle_status • deep archive • deleted • glacier • infrequent access • standard ← default | enum of string • default: standard | Current S3 storage class of this object. [Files in Standard and Infrequent Access are accessible without restriction. Files in Glacier and Deep Archive need to be requested and cannot be downloaded] |
| sequencing_center | SubmissionCenter • string | Sequencing Center. See values here |
| status • archived • deleted • in review • obsolete • public • released • restricted • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| submission_centers | SubmissionCenter • array of string • unique | Submission Centers that created this item. See values here |
| tags | array of string • min string length: 1 • max string length: 50 • unique • restricted | Key words that can tag an item - useful for filtering. Must adhere to (regex) pattern: ^[a-zA-Z0-9_-]+$ |
| upload_credentials | object • calculated | - |
| upload_key | string • calculated | File object name in S3. |
| uuid | string | Unique ID by which this object is identified. |