# Custom Config Support

## Local App Setup

## Overview

This document describes how to use the **Custom Configuration Support** feature for the pipeline software. This feature allows users to customize a specific set of DRAGEN command-line options to override the default values pre-defined in the pipeline.

## Customization with `customConfig` and `customResourceDir`

Users can customize pipeline behavior and file inputs using:

* `--customConfig` : path to a **custom configuration file** listing customized parameter values.
* `--customResourceDir` : path to a **directory** containing custom resource files.

Both options should be used together if file-based overrides are required.

## Important note for using File Parameters

* For **file parameters** (parameters that require a file), users must specify **relative paths** in the `customConfig` file. The software will join `customResourceDir` and the relative path to form the full file path.
* Additionally, the value assigned to a **file parameter** must be enclosed in single quotes (`''`).

## Examples

### Command Line

```bash
run_Solid_WGS_TN_{version}.sh \
--inputType bcl \
--inputFolder /staging/input-folder \
--customConfig /path/to/solid_custom_param.config \
--customResourceDir /path/to/custom_resources_solid_dir
```

### `solid_custom_param.config` Content

```bash
## custom parameters
somatic_vc_output_evidence_bam = false
germline_vc_output_evidence_bam = false

somatic_qc_detect_contamination = true

somatic_aligner_clip_pe_overhang = 0
germline_aligner_clip_pe_overhang = 0

## custom reference files
somatic_vc_systematic_noise = '/snv/WGS_hg38_v1.0_systematic_noise.snv.bed.gz'
somatic_sv_systematic_noise = '/sv/WGS_FF_solid_hg38_v1.0_systematic_noise.sv.bedpe.gz'
somatic_vc_somatic_hotspots = '/snv/somatic_hotspots_GRCh38.vcf.gz'
```

### `custom_resources_solid_dir` Folder Structure

```
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
```

## `customConfig` Template (with default value)

```bash

cram_reference = 'genome.fa'

#cram_reference_path ='/testing_data_cram/genome_fasta/hs37d5_chr/'
#tumor normal caller settings
#somatic_msi_coverage_threshold = 40
#somatic_msi_microsatellites_file = ''
#somatic_vc_combine_phased_variants_distance = 2
#somatic_vc_output_evidence_bam = false
#somatic_qc_detect_contamination = true
#somatic_qc_coverage_ignore_overlaps = false
#somatic_aligner_clip_pe_overhang = 0
#somatic_sv_ins_tandup_hotspot_regions_bed = ''
#somatic_sv_systematic_noise = ''
#somatic_vc_somatic_hotspots = ''
#somatic_vc_target_vaf = 0.03
#somatic_vc_sq_filter_threshold = 3
#somatic_vc_systematic_noise = ''
#somatic_vc_excluded_regions_bed = ''

#germline caller settings
#germline_vc_output_evidence_bam = false
#germline_qc_detect_contamination = true
#germline_qc_coverage_ignore_overlaps = false
#germline_aligner_clip_pe_overhang = 0
#germline_vc_combine_phased_variants_distance = 2

```


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