Environment Variables

All SeqDesk environment variables use the SEQDESK_ prefix. They have the highest priority in the configuration resolution order, overriding config file and database values.

Value Parsing

Environment variables are parsed according to their target type:

Booleans — "true" / "false" (case-insensitive)
Numbers — parsed as integers for fields like scanDepth, cores, sessionTimeout
Arrays — comma-separated values, e.g. ".fastq.gz,.fq.gz,.fastq,.fq"
Strings — all other values

Site Settings

Variable	Config Path	Type	Default	Description
`SEQDESK_SITE_NAME`	`site.name`	string	`"SeqDesk"`	Display name of the facility
`SEQDESK_DATA_PATH`	`site.dataBasePath`	string	`"./data"`	Base path for sequencing data storage
`SEQDESK_CONTACT_EMAIL`	`site.contactEmail`	string	—	Facility contact email address

Pipeline Settings

Variable	Config Path	Type	Default	Description
`SEQDESK_PIPELINES_ENABLED`	`pipelines.enabled`	boolean	`false`	Master switch for all pipeline features
`SEQDESK_PIPELINE_RUN_DIR`	`pipelines.execution.runDirectory`	string	`"./pipeline_runs"`	Output directory for pipeline runs
`SEQDESK_PIPELINE_MODE`	`pipelines.execution.mode`	enum	`"local"`	Execution mode: `local`, `slurm`, or `kubernetes`

Conda

Variable	Config Path	Type	Default	Description
`SEQDESK_CONDA_ENABLED`	`pipelines.execution.conda.enabled`	boolean	`false`	Use Conda for pipeline dependencies
`SEQDESK_CONDA_PATH`	`pipelines.execution.conda.path`	string	`"/opt/conda"`	Path to Conda installation
`SEQDESK_CONDA_ENV`	`pipelines.execution.conda.environment`	string	—	Conda environment name

SLURM

Variable	Config Path	Type	Default	Description
`SEQDESK_SLURM_ENABLED`	`pipelines.execution.slurm.enabled`	boolean	`false`	Enable SLURM job submission
`SEQDESK_SLURM_QUEUE`	`pipelines.execution.slurm.queue`	string	`"default"`	SLURM partition/queue name
`SEQDESK_SLURM_CORES`	`pipelines.execution.slurm.cores`	integer	`4`	CPU cores per job
`SEQDESK_SLURM_MEMORY`	`pipelines.execution.slurm.memory`	string	`"16GB"`	Memory per job
`SEQDESK_SLURM_TIME`	`pipelines.execution.slurm.timeLimit`	integer	`24`	Time limit in hours

MAG Pipeline

Variable	Config Path	Type	Default	Description
`SEQDESK_MAG_ENABLED`	`pipelines.mag.enabled`	boolean	`true`	Enable nf-core/mag pipeline
`SEQDESK_MAG_VERSION`	`pipelines.mag.version`	string	`"3.4.0"`	nf-core/mag pipeline version
`SEQDESK_MAG_STUB`	`pipelines.mag.stubMode`	boolean	`false`	Use stub mode (test mode, no real analysis)

ENA Submission

Variable	Config Path	Type	Default	Description
`SEQDESK_ENA_TEST_MODE`	`ena.testMode`	boolean	`true`	Use ENA test server instead of production
`SEQDESK_ENA_USERNAME`	`ena.username`	string	—	Webin account username
`SEQDESK_ENA_PASSWORD`	`ena.password`	string	—	Webin account password
`SEQDESK_ENA_CENTER`	`ena.centerName`	string	`""`	Submission center name

Always set ENA credentials through environment variables or the Admin UI — never commit them to a config file.

Sequencing Files

Variable	Config Path	Type	Default	Description
`SEQDESK_FILES_EXTENSIONS`	`sequencingFiles.extensions`	array	`".fastq.gz,.fq.gz,.fastq,.fq"`	Allowed file extensions (comma-separated)
`SEQDESK_FILES_SCAN_DEPTH`	`sequencingFiles.scanDepth`	integer	`2`	Directory scan depth (1–10)
`SEQDESK_FILES_SINGLE_END`	`sequencingFiles.allowSingleEnd`	boolean	`true`	Allow single-end reads

Authentication

Variable	Config Path	Type	Default	Description
`SEQDESK_AUTH_REGISTRATION`	`auth.allowRegistration`	boolean	`true`	Allow public user registration
`SEQDESK_SESSION_TIMEOUT`	`auth.sessionTimeout`	integer	`24`	Session timeout in hours

Runtime Variables

These standard environment variables are used by the application runtime. They can also be set in the runtime section of the config file — if not already present as environment variables, the config file values are applied to process.env at startup.

Variable	Config Path	Description
`DATABASE_URL`	`runtime.databaseUrl`	PostgreSQL runtime connection string
`DIRECT_URL`	`runtime.directUrl`	Direct PostgreSQL connection for Prisma migrations
`NEXTAUTH_URL`	`runtime.nextAuthUrl`	NextAuth.js callback URL (e.g. `http://localhost:3000`)
`NEXTAUTH_SECRET`	`runtime.nextAuthSecret`	Session signing secret (generate with `openssl rand -base64 32`)
`SEQDESK_UPDATE_SERVER`	`runtime.updateServer`	Update server URL (default: `https://seqdesk.com`)

Examples

Set variables in your shell, .env file, or deployment system:


# Site
export SEQDESK_SITE_NAME="My Sequencing Facility"
export SEQDESK_DATA_PATH="/mnt/sequencing/data"
 
# ENA (use env vars for secrets)
export SEQDESK_ENA_USERNAME="Webin-12345"
export SEQDESK_ENA_PASSWORD="your-password"
export SEQDESK_ENA_TEST_MODE="false"
 
# SLURM cluster
export SEQDESK_PIPELINE_MODE="slurm"
export SEQDESK_SLURM_ENABLED="true"
export SEQDESK_SLURM_QUEUE="bioinformatics"
export SEQDESK_SLURM_CORES="16"
export SEQDESK_SLURM_MEMORY="64GB"