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AdministrationData Storage

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 → Data Compute or Settings
  • Config file — sequencingFiles section
  • Environment variables — SEQDESK_FILES_* and SEQDESK_DATA_PATH

Settings Reference

SettingEnv VariableDefaultDescription
Data Base PathSEQDESK_DATA_PATH./dataRoot directory for sequencing data
File ExtensionsSEQDESK_FILES_EXTENSIONS.fastq.gz,.fq.gz,.fastq,.fqAllowed file types
Scan DepthSEQDESK_FILES_SCAN_DEPTH2Directory levels to search (1–10)
Allow Single-EndSEQDESK_FILES_SINGLE_ENDtrueInclude unpaired reads
Ignore Patterns—**/tmp/**, **/undetermined/**Glob patterns to skip

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:

  1. Path validation — checks the directory exists and is readable
  2. File count — shows how many matching files are found
  3. 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