# Launching Analysis

## 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 [Command-Line Options](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/installation/launching-analysis/command-line-options).

#### 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 [Sample Sheet Requirements](https://help.dragen.illumina.com/dragen-v4.4/product-guide/dragen-v4.4/dragen-apps/dragen-heme-wgs-to-pipeline/quick-start/sample-sheet-requirements)). If the `--sampleSheet` argument is not provided, the software checks for a file named `SampleSheet.csv` in the input folder.

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.