Overview

Run on DRAGEN Server

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 .

Getting Started

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 argument must also be provided with the absolute path to a valid Sample Sheet (refer to

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.

Overview

Command line options

For command-line options, refer to Table 1: Shell Script Command-Line Options for details.

Local output management

Common output files for cloud and local pipelines are described in the .

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