CLI Reference

This document provides a comprehensive reference for all command-line options available in the Varvis Download CLI.

Usage

varvis-download [options]

Options

Option	Type	Default	Description
--config, c	string	.config.json	Path to the configuration file
--username, u	string	-	Varvis API username
--password, p	string	-	Varvis API password
--target, t	string	-	Target for the Varvis API
--analysisIds, a	string	-	Analysis IDs to download files for (comma-separated)
--sampleIds, s	string	-	Sample IDs to filter analyses (comma-separated)
--limsIds, l	string	-	LIMS IDs to filter analyses (comma-separated)
--list, L	boolean	false	List available files for the specified analysis IDs
--destination, d	string	.	Destination folder for the downloaded files
--proxy, x	string	-	Proxy URL
--proxyUsername, pxu	string	-	Proxy username
--proxyPassword, pxp	string	-	Proxy password
--overwrite, o	boolean	false	Overwrite existing files
--filetypes, f	string	bam,bam.bai	File types to download (comma-separated)
--loglevel, ll	string	info	Logging level (info, warn, error, debug)
--logfile, lf	string	-	Path to the log file
--reportfile, r	string	-	Path to the report file
--filter, F	array	[]	Filter expressions (e.g., "analysisType=SNV", "sampleId>LB24-0001")
--range, g	string	-	Genomic range for ranged download (e.g., chr1:1-100000)
--bed, b	string	-	Path to BED file containing multiple regions
--restoreArchived, ra	string	ask	Restore archived files. Accepts "no", "ask" (default), "all", or "force".
--restorationFile, rf	string	awaiting-restoration.json	Path and name for the awaiting-restoration JSON file
--resumeArchivedDownloads, rad	boolean	false	Resume downloads for archived files from the awaiting-restoration JSON file if restoreEstimation has passed.
--version, v	boolean	false	Show version information
--help, h	boolean	false	Show help

Examples

Basic Usage

# Download BAM files for specific analysis IDs
varvis-download -u username -p password -t target -a "analysis1,analysis2"

# List available files without downloading
varvis-download -u username -p password -t target -a "analysis1" --list

# Download with custom destination
varvis-download -u username -p password -t target -a "analysis1" -d "/path/to/download"

Advanced Usage

# Download with filters
varvis-download -u username -p password -t target -s "sample1,sample2" --filter "analysisType=SNV"

# Ranged download for specific genomic region
varvis-download -u username -p password -t target -a "analysis1" --range "chr1:1-100000"

# Download with BED file for multiple regions
varvis-download -u username -p password -t target -a "analysis1" --bed "/path/to/regions.bed"

# Resume archived downloads
varvis-download --resumeArchivedDownloads

Configuration File

You can use a configuration file to store commonly used options:

varvis-download --config /path/to/config.json

Example configuration file:

{
  "username": "your-username",
  "target": "https://your-varvis-instance.com",
  "destination": "/path/to/downloads",
  "filetypes": "bam,bam.bai,vcf",
  "loglevel": "info"
}