Data Model

SeqDesk uses Prisma ORM with PostgreSQL. This page describes the core entities and their relationships.

Entity Relationship Overview


User ──< Order ──< Sample >── Study
  │                  │           │
  │                  ├── Read    ├── PipelineRun ──< PipelineRunStep
  │                  │                │
  │                  ├── Assembly     ├── PipelineRunEvent
  │                  │                │
  │                  └── Bin          └── PipelineArtifact
  │
  ├── Department
  └── AdminInvite

Core Models

User

Field	Type	Description
id	String	Primary key (CUID)
email	String	Unique login identifier
password	String	bcrypt hash
firstName, lastName	String	Display name
role	String	`RESEARCHER` or `FACILITY_ADMIN`
researcherRole	String?	PI, POSTDOC, PHD_STUDENT, MASTER_STUDENT, TECHNICIAN, OTHER
institution	String?	Research institution
departmentId	String?	Foreign key to Department

Order

Field	Type	Description
id	String	Primary key (CUID)
orderNumber	String	Unique, format: `ORD-YYYYMMDD-XXXX`
name	String?	Descriptive name
status	String	`DRAFT`, `SUBMITTED`, or `COMPLETED`
platform	String?	ILLUMINA, OXFORD_NANOPORE, PACBIO, etc.
libraryStrategy	String?	WGS, RNA-Seq, AMPLICON, etc.
librarySource	String?	GENOMIC, METAGENOMIC, etc.
customFields	String?	JSON for form builder fields
userId	String	Foreign key to User

Sample

Field	Type	Description
id	String	Primary key (CUID)
sampleId	String	Internal ID (format: `S-{timestamp}-{random}`)
sampleAlias	String?	User-friendly alias
scientificName	String?	Taxonomic name
taxId	String?	NCBI taxonomy ID
checklistData	String?	JSON — MIxS metadata
checklistUnits	String?	JSON — units for metadata
customFields	String?	JSON — custom form fields
orderId	String	Foreign key to Order
studyId	String?	Foreign key to Study (optional)

Study

Field	Type	Description
id	String	Primary key (CUID)
title	String	Study title
alias	String?	Unique alias for ENA
checklistType	String?	MIxS checklist type
studyAccessionId	String?	ENA accession (PRJEB…)
submitted	Boolean	Whether submitted to ENA
readyForSubmission	Boolean	Marked ready by user
userId	String	Foreign key to User (owner)

Read

Field	Type	Description
id	String	Primary key (CUID)
file1	String?	Forward reads path (R1)
file2	String?	Reverse reads path (R2)
checksum1, checksum2	String?	MD5 checksums
experimentAccessionNumber	String?	ENA experiment (ERX…)
runAccessionNumber	String?	ENA run (ERR…)
sampleId	String	Foreign key to Sample
sequencingRunId	String?	Foreign key to SequencingRun

PipelineRun

Field	Type	Description
id	String	Primary key (CUID)
runNumber	String	Unique, format: `{PIPELINE}-{DATE}-{NNN}`
pipelineId	String	Pipeline identifier (e.g., `mag`)
status	String	pending, queued, running, completed, failed, cancelled
progress	Int	0–100
studyId	String	Foreign key to Study
userId	String	Foreign key to User (who started it)
runFolder	String	Path to run directory

Assembly

Field	Type	Description
id	String	Primary key (CUID)
assemblyName	String	Assembly identifier
assemblyFile	String	Path to FASTA file
assemblyAccession	String?	ENA accession
sampleId	String	Foreign key to Sample
createdByPipelineRunId	String	Foreign key to PipelineRun

Bin

Field	Type	Description
id	String	Primary key (CUID)
binName	String	Bin identifier
binFile	String	Path to bin FASTA
completeness	Float	CheckM completeness (0–100)
contamination	Float	CheckM contamination (0–100)
sampleId	String	Foreign key to Sample
createdByPipelineRunId	String	Foreign key to PipelineRun

Supporting Models

Model	Purpose
Department	User grouping with name, description, isActive
AdminInvite	Invite codes for admin registration
StatusNote	Audit trail on orders (STATUS_CHANGE, SAMPLES_SENT, INTERNAL)
Sampleset	MIxS checklist configuration per order
SequencingRun	Run-level metadata and QC metrics
SiteSettings	Singleton configuration (branding, ENA, modules)
OrderFormConfig	Order form field definitions
PipelineConfig	Per-pipeline enabled flag and settings
PipelineRunStep	Individual process status within a run
PipelineRunEvent	Event log from weblog/trace
PipelineArtifact	Output files with metadata
Submission	ENA submission tracking per entity