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.

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