Common output files for cloud and local pipelines are described in the Analysis Output.
On DRAGEN server, Nextflow logs are contained in the Work folder in a hierarchical folder structure organized by the tasks in the pipeline_trace.txt. These files are prefixed with "." and hidden from normal view.
📂 Work — (DRAGEN server only) - Contains information and files related to Nextflow execution
📄 .command.log - Contains Nextflow pipeline step execution log.
📄 .command.out - Contains Nextflow pipeline step standard output log.
📄 .command.err - Contains Nextflow pipeline step standard error log.
📄 .exit.code - Contains Nextflow pipeline step execution exit code.
For command-line options, refer to Table 1: Shell Script Command-Line Options for details.
CAUTION: Do not run analyses as the root user as it can lead to permissions issues when managing data generated by the software.
--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.
--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.
The DRAGEN Heme WGS Tumor Only Pipeline is launched with the bash script called run_Heme_WGS_TO_{version}.sh, which is installed in the /usr/local/bin directory. The bash script is executed on the command line and runs the software using DRAGEN Application Manager. For a full list of command-line options, refer to .
To launch an analysis, you must provide the --inputType and --inputFolder arguments. The --inputType argument can be bcl, fastq, bam, or cram. When starting from a sequencing system run folder containing BCL files, --inputType must be bcl and --inputFolder is the absolute path to the full run folder. When starting from FASTQ, BAM, or CRAM files --inputFolder may also be a comma separated list of folders. If more than one input folder is specified, the --sampleSheet
Analysis output is written to /staging/DRAGEN_Heme_WGS_Tumor_Only_Pipeline_{version}_Analysis_{datetimestamp} by default. To write to a different output directory, run the bash script with --analysisFolder <FULL_PATH_TO_ANALYSIS_FOLDER>.
The --demultiplexOnly flag runs the pipeline through FASTQ Generation only, and these outputs can be used for splitting a run into smaller batch analyses with --inputType fastq and the --sampleIDs argument.
--sampleSheet argument is not provided, the software checks for a file named SampleSheet.csv in the input folder.