Command Line Options

Overview

Command line options

For command-line options, refer to Table 1 (below) for details.

By default, analysis output is written to the /staging/DRAGEN_Solid_WGS_TN_4.4.4_Analysis_ directory. To write to a different output directory, run the bash script with the following argument

Table 1: Shell Script Command-Line Options

CAUTION: Do not run analyses as the root user as it can lead to permissions issues when managing data generated by the software.

Argument>	Required	Description
--runFolder	Not required when running from FASTQ files. Required when running from BCL files.	Full path to the sequencing system run folder that contains SampleSheet.csv, RunInfo.xml, RunParameters.xml, CopyComplete.txt, and the Data directory.
--fastqFolder	Not required	Full path to an existing FASTQ folder. FASTQ files can be when running contained in a single folder or organized into folders by BCL files. Sample ID. Required when running from FASTQ files.
‑‑analysisFolder	No	Full path to the alternative analysis folder. Default is /staging/DRAGEN_TSO500_CTDNA_2.6.0_Analysis_ if not specified. This folder must have enough available free space for the analysis and be on an NVMe SSD partition to achieve high performance.
--sampleSheet	No	Full path to the sample sheet file. If the sample sheet is named SampleSheet.csv and is located in the run or fastq folder (depending on how the analysis is initiated), this command is not required.
--sampleIDs	No	The comma-delimited sample IDs that are processed by the run. For example, Sample_1,Sample_2.
--version	No	Displays the version of the software, and then exits.
--help	No