# Command Line Options

## Overview

### Command line options

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

### 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                                                                                                                                                                                                                                                                                     |
| ----------------------- | -------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| --inputType             | Yes      | Possible values include fastq, bam, cram.                                                                                                                                                                                                                                                       |
| --inputFolder           | Yes      | Input folder containing {input type} files. Multiple folders can be specified as a comma separated list.                                                                                                                                                                                        |
| --sampleSheet           | No       | Full path to the sample sheet file. If the sample sheet is named SampleSheet.csv and is located in the single input folder (depending on how the analysis is initiated), this command is not required.                                                                                          |
| --analysisFolder        | No       | Full path to the alternative analysis folder. Default is `/staging/DRAGEN_Solid_WGS_Tumor_Normal_Pipeline_{version}_Analysis_{datetimestamp}` 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. |
| --sampleOrCaseIDs       | No       | The comma-delimited sample IDs (or CaseID) that are processed by the run. For example, Sample\_1,Sample\_2.                                                                                                                                                                                     |
| --referenceGenome       | No       | Specify the reference genome to use for alignment. Possible values: hg38 or hs37d5\_chr. Default is hg38.                                                                                                                                                                                       |
| --disableOraCompression | No       | Specify to disable Ora compression.                                                                                                                                                                                                                                                             |
| --customResourceDir     | No       | Provide custom resource directory path.                                                                                                                                                                                                                                                         |
| --customConfig          | No       | Provide custom config file path.                                                                                                                                                                                                                                                                |
| --keepFullWorkDir       | No       | Copy entire work dir to analysis output folder. Default behavior is to copy only nextflow logs.                                                                                                                                                                                                 |
| --version               | No       | Displays the version of the software, and then exits.                                                                                                                                                                                                                                           |
| --help                  | No       | Displays the help text.                                                                                                                                                                                                                                                                         |