# Custom Config Support

This feature allows users to customize a specific set of DRAGEN command-line options to override the default values pre-defined in the pipeline.

## ICA Setup

On the ICA (Illumina Connected Analytics) user interface (UI) to the software, you can specify the **Custom Parameters Config File** and **Custom Resources Directory** directly. Supported customizable options are described below.

## Examples

### `heme_custom_param.config` Content

```groovy
## custom parameters
vc_output_evidence_bam = false
qc_detect_contamination = true
aligner_clip_pe_overhang = 0

## custom reference files
vc_systematic_noise = '/snv/WGS_hg38_v1.0_systematic_noise.snv.bed.gz'
sv_systematic_noise = '/sv/WGS_FF_Heme_hg38_v1.0_systematic_noise.sv.bedpe.gz'
vc_somatic_hotspots = '/snv/somatic_hotspots_GRCh38.vcf.gz'
```

### `custom_resources_Heme_dir` Folder Structure on ICA

```
custom_resources_Solid/
├── snv
│   ├── WGS_Solid_hg38_v1.0_systematic_noise.snv.bed.gz
│   └── somatic_hotspots_GRCh38.vcf.gz
└── sv
    └── WGS_Solid_FF_solid_hg38_v1.0_systematic_noise.sv.bedpe.gz
```

> **ℹ️ Note:** Custom resource files and the custom configuration file must be uploaded to the same ICA project where the run is created. You can use the `icav2` client or other supported methods. See [Data Transfer Options with ICA Platform](https://help.ica.illumina.com/tutorials/datatransfer) for details.

### ICA Input Files UI Example

![ICA Setup Screenshot](https://25033470-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FG9szlFZupV6Q2DasL98y%2Fuploads%2Fgit-blob-9b4fa1663c6eb80582787f4d7dc254caf95d47d0%2Fica-setup-screenshot.png?alt=media)