Config File Reference

The config file provides project-level configuration in a single structured JSON file. It is the recommended way to manage non-secret settings.

File Discovery

SeqDesk searches for config files in the project root (same directory as package.json) in this order:

seqdesk.config.json (recommended)
.seqdeskrc
.seqdeskrc.json

The first file found is used. If no config file exists, only environment variables, database settings, and built-in defaults apply.

Complete Structure


{
  "site": {
    "name": "My Sequencing Facility",
    "dataBasePath": "/mnt/sequencing/data",
    "contactEmail": "facility@example.com"
  },
 
  "pipelines": {
    "enabled": true,
    "execution": {
      "mode": "local",
      "runDirectory": "./pipeline_runs",
      "conda": {
        "enabled": true,
        "path": "/opt/conda",
        "environment": "seqdesk-pipelines"
      },
      "slurm": {
        "enabled": false,
        "queue": "default",
        "cores": 4,
        "memory": "16GB",
        "timeLimit": 24,
        "options": ""
      }
    },
    "mag": {
      "enabled": true,
      "version": "3.4.0",
      "stubMode": false,
      "skipProkka": true,
      "skipConcoct": true
    }
  },
 
  "ena": {
    "testMode": true,
    "username": "",
    "password": "",
    "centerName": ""
  },
 
  "sequencingFiles": {
    "extensions": [".fastq.gz", ".fq.gz", ".fastq", ".fq"],
    "scanDepth": 2,
    "allowSingleEnd": true,
    "ignorePatterns": ["**/tmp/**", "**/undetermined/**"]
  },
 
  "auth": {
    "allowRegistration": true,
    "requireEmailVerification": false,
    "sessionTimeout": 24
  },
 
  "runtime": {
    "databaseUrl": "postgresql://seqdesk:replace-with-password@127.0.0.1:5432/seqdesk?schema=public",
    "directUrl": "postgresql://seqdesk:replace-with-password@127.0.0.1:5432/seqdesk?schema=public",
    "nextAuthUrl": "http://localhost:3000",
    "nextAuthSecret": "your-secret-here"
  }
}

Section Reference

`site` — Facility Information

Key	Type	Default	Description
`name`	string	`"SeqDesk"`	Display name shown in the UI
`dataBasePath`	string	`"./data"`	Base directory for sequencing data
`contactEmail`	string	—	Contact email shown to researchers

`pipelines` — Pipeline Configuration

Key	Type	Default	Description
`enabled`	boolean	`false`	Master switch for pipeline features

`pipelines.execution` — Execution Settings

Key	Type	Default	Description
`mode`	`"local"` \| `"slurm"` \| `"kubernetes"`	`"local"`	Where pipelines run
`runDirectory`	string	`"./pipeline_runs"`	Output directory

`pipelines.execution.conda` — Conda Settings

Key	Type	Default	Description
`enabled`	boolean	`false`	Use Conda for dependencies
`path`	string	`"/opt/conda"`	Conda installation path
`environment`	string	—	Environment name

`pipelines.execution.slurm` — SLURM Settings

Key	Type	Default	Description
`enabled`	boolean	`false`	Submit jobs to SLURM
`queue`	string	`"default"`	Partition/queue name
`cores`	integer	`4`	CPUs per job
`memory`	string	`"16GB"`	Memory per job
`timeLimit`	integer	`24`	Time limit (hours)
`options`	string	`""`	Additional SLURM options

`pipelines.mag` — MAG Pipeline

Key	Type	Default	Description
`enabled`	boolean	`true`	Enable nf-core/mag
`version`	string	`"3.4.0"`	Pipeline version
`stubMode`	boolean	`false`	Test mode (no real analysis)
`skipProkka`	boolean	`true`	Skip Prokka annotation
`skipConcoct`	boolean	`true`	Skip CONCOCT binning

`ena` — ENA Submission

Key	Type	Default	Description
`testMode`	boolean	`true`	Use test server
`username`	string	—	Webin username
`password`	string	—	Webin password
`centerName`	string	`""`	Submission center name

Avoid storing ENA credentials in the config file. Use environment variables (SEQDESK_ENA_USERNAME, SEQDESK_ENA_PASSWORD) or the Admin UI instead.

`sequencingFiles` — File Discovery

Key	Type	Default	Description
`extensions`	string[]	`[".fastq.gz", ".fq.gz", ".fastq", ".fq"]`	Allowed file extensions
`scanDepth`	integer	`2`	Directory scan depth (1–10)
`allowSingleEnd`	boolean	`true`	Allow single-end reads
`ignorePatterns`	string[]	`["/tmp/", "/undetermined/"]`	Glob patterns to skip

`auth` — Authentication

Key	Type	Default	Description
`allowRegistration`	boolean	`true`	Public registration enabled
`requireEmailVerification`	boolean	`false`	Require email verification
`sessionTimeout`	integer	`24`	Session timeout (hours)

`runtime` — Application Runtime

These values are applied to process.env at startup if the corresponding environment variable is not already set.

Key	Maps To	Description
`databaseUrl`	`DATABASE_URL`	PostgreSQL runtime connection string
`directUrl`	`DIRECT_URL`	Direct PostgreSQL connection for Prisma migrations
`nextAuthUrl`	`NEXTAUTH_URL`	NextAuth.js callback URL
`nextAuthSecret`	`NEXTAUTH_SECRET`	Session signing secret
`updateServer`	`SEQDESK_UPDATE_SERVER`	Update server URL

Validation

The config system validates:

The file must be valid JSON
site.dataBasePath must be a string
pipelines.execution.mode must be local, slurm, or kubernetes
ena.testMode must be a boolean
sequencingFiles.scanDepth must be an integer between 1 and 10

Invalid values are logged as warnings and the corresponding default is used instead.

Config File Reference

File Discovery

Complete Structure

Section Reference

site — Facility Information

pipelines — Pipeline Configuration

pipelines.execution — Execution Settings

pipelines.execution.conda — Conda Settings

pipelines.execution.slurm — SLURM Settings

pipelines.mag — MAG Pipeline

ena — ENA Submission

sequencingFiles — File Discovery

auth — Authentication

runtime — Application Runtime