> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/setup/advanced/custom_config.md).

# 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.

## Cloud Setup

On the Platform Core 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 Platform Core

```
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 Platform Core project where the run is created. You can use the `icav2` client or other supported methods. See [Data Transfer Options with Platform Core](https://help.ica.illumina.com/tutorials/datatransfer) for details.

### Platform Core Input Files UI Example

![Platform Core Run Setup Screenshot](https://2414276024-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FjdZwGT2DsEhB6cr9Abe8%2Fuploads%2Fgit-blob-9b4fa1663c6eb80582787f4d7dc254caf95d47d0%2Fica-setup-screenshot.png?alt=media)


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation by asking a question.

Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters:

```
GET https://help.bioinsight.illumina.com/dragen-clinical-research-apps/readme/dragen-heme-wgs-to-pipeline/setup/advanced/custom_config.md?ask=<question>&goal=<user_goal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.