Command Line Options

Overview

Command line options

For command-line options, refer to Table 1: Shell Script Command-Line Options 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 bcl, fastq, bam, cram.
--inputFolder	Yes	Input folder containing {input type} files. Multiple {input type, except bcl} 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 run or fastq 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_Heme_WGS_Tumor_Only_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.
--sampleIDs	No	The comma-delimited sample IDs 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.
--demultiplexOnly	No	Demultiplex to generate FASTQ files only without further analysis.
--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.