Data Storage

Data storage settings control where SeqDesk looks for sequencing files and how it discovers them.

Configuration

These settings can be configured through:

Admin UI — at Admin → Infrastructure → Data Storage (/admin/data-storage). The Infrastructure page (/admin/data-compute) itself is a read-only validation hub; editing happens on the linked Data Storage page.
Config file — sequencingFiles section
Environment variables — SEQDESK_FILES_* and SEQDESK_DATA_PATH

Only Data Base Path and Allowed File Extensions are editable in the admin UI. The remaining settings are set through the config file or environment variables only.

Settings Reference

Setting	UI-editable	Env Variable	Default	Description
Data Base Path	Yes	`SEQDESK_DATA_PATH`	`./data`	Root directory for sequencing data
Allowed File Extensions	Yes (Advanced)	`SEQDESK_FILES_EXTENSIONS`	`.fastq.gz,.fq.gz,.fastq,.fq`	Allowed file types
Scan Depth	No	`SEQDESK_FILES_SCAN_DEPTH`	`2`	Directory levels to search (1–10)
Allow Single-End	No (forced)	—	`true`	Always `true`; unpaired reads are always included
Ignore Patterns	No	—	—	Glob patterns to skip

Allow Single-End is forced to true by the application — it is not exposed in the UI or as a configurable setting, and unpaired reads are always discovered. Scan Depth and Ignore Patterns are config-file only and do not appear in the admin UI.

Data Base Path

The base path is the root directory where your sequencing data is stored. SeqDesk scans this directory for FASTQ files.

Requirements:

The path must be readable by the SeqDesk process
SeqDesk accesses files read-only — it never modifies or deletes sequencing data
Use absolute paths in production (e.g., /mnt/sequencing/data)

Scan Depth

Controls how many directory levels the scanner descends:

Depth 1 — only the base path itself
Depth 2 (default) — base path + one level of subdirectories
Depth 10 — deepest supported scan

Higher depth values scan more files but take longer. Set this based on your directory structure.

Testing the Configuration

In the admin settings, use the test feature to verify your configuration:

Path validation — checks the directory exists and is readable
File count — shows how many matching files are found
Simulation — previews what the scanner would discover

This helps catch permission issues or incorrect paths before using them in production.

Security

File access is restricted to the configured base path:

All file paths are validated against the base path
Path traversal (../) is blocked
Symlinks are followed only if they resolve within the base path
The file API only serves files with allowed extensions