Configuration Schema

This document describes the configuration file schema for the Varvis Download CLI.

Overview

The configuration file is a JSON file that can contain any of the CLI options to avoid having to specify them on the command line each time. Command line arguments take precedence over configuration file values.

Default Configuration File

By default, the tool looks for a configuration file named .config.json in the current directory. You can specify a different configuration file using the --config option.

Schema

Property	Type	Required	Default	Description
username	string	No	-	Varvis API username
password	string	No	-	Varvis API password
target	string	No	-	Target for the Varvis API (instance short name, e.g. laborberlin)
destination	string	No	.	Destination folder for downloaded files
proxy	string	No	-	Proxy URL for HTTP requests
proxyUsername	string	No	-	Username for proxy authentication
proxyPassword	string	No	-	Password for proxy authentication
overwrite	boolean	No	false	Whether to overwrite existing files
filetypes	string	No	bam,bam.bai	Comma-separated list of file types to download
loglevel	string	No	info	Logging level (info, warn, error, debug)
logfile	string	No	-	Path to the log file
reportfile	string	No	-	Path to the report file
restoreArchived	string	No	ask	Restore archived files behavior ("no", "ask", "all", "force")
restorationFile	string	No	awaiting-restoration.json	Path for the restoration tracking file
filter	array	No	[]	Filter expressions (AND logic); operators = != > < >= <= ~= ^=
latest	boolean	No	false	Keep only the newest analysis per sample
range	string	No	-	Genomic range for ranged download (e.g. chr1:1-100000)
bed	string	No	-	Path to a BED file with multiple regions
unmapped	boolean	No	false	Extract unmapped reads from BAM files (cannot combine with bed)
list	boolean	No	false	List available files instead of downloading
listUrls	boolean	No	false	Print direct download URLs instead of downloading
urlFile	string	No	-	File to save URLs when listUrls is set
passwordStdin	boolean	No	false	Read the password from the first line of stdin

Example Configuration Files

Basic Configuration

{
  "username": "your-username",
  "target": "mytarget",
  "destination": "/path/to/downloads"
}

Advanced Configuration

{
  "username": "your-username",
  "target": "production-server",
  "destination": "/data/downloads",
  "proxy": "http://proxy.company.com:8080",
  "proxyUsername": "proxy-user",
  "filetypes": "bam,bam.bai,vcf.gz,vcf.gz.tbi",
  "overwrite": false,
  "loglevel": "debug",
  "logfile": "/var/log/varvis-download.log",
  "restoreArchived": "ask"
}

Minimal Configuration

{
  "username": "your-username",
  "target": "mytarget"
}

File Types

The filetypes property accepts a comma-separated list of file extensions. Common values include:

• bam - Binary Alignment Map files
• bam.bai - BAM index files
• vcf.gz - Compressed VCF files
• vcf.gz.tbi - Tabix index files for compressed VCF

Target Specification

The target property is the Varvis instance short name (for example laborberlin or mytarget), which the tool expands to the instance host — not a full URL.

Logging Levels

Available logging levels (from most to least verbose):

• debug - Detailed debugging information
• info - General information (default)
• warn - Warning messages only
• error - Error messages only

Archive Restoration Modes

The restoreArchived property controls how archived files are handled:

• no - Skip archived files entirely
• ask - Prompt for each archived file (default)
• all - Ask once, then restore all archived files
• force - Automatically restore all archived files without prompting