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

run_Heme_WGS_TO_{version}.sh \
  --inputType bcl \
  --inputFolder /heme_input_bcl \
  --customConfig /path/heme_custom_param.config \
  --customResourceDir custom_resources_Heme_dir

heme_custom_param.config Content

# 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

custom_resources_Heme/
├── snv
│   ├── WGS_hg38_v1.0_systematic_noise.snv.bed.gz
│   └── somatic_hotspots_GRCh38.vcf.gz
└── sv
    └── WGS_FF_Heme_hg38_v1.0_systematic_noise.sv.bedpe.gz

customConfig Template (with default value)

#vc_systematic_noise = ''
#enable_map_align = true
#sv_systematic_noise = ''
#vc_output_evidence_bam = false
#qc_detect_contamination = true
#vc_somatic_hotspots = ''
#sv_somatic_ins_tandup_hotspot_regions_bed = ''
#cram_reference = ''
#aligner_clip_pe_overhang = 0

Supported Parameters

Display Name	Parameter Name	Component	Allowed Values	Default Value	Optional
VC Systematic Noise File	vc_systematic_noise	Variant Caller	file	included	Yes
VC Somatic Hotspots File	vc_somatic_hotspots	Variant Caller	file	included	Yes
CRAM Input Reference Genome	cram_reference	Mapper	file	included	Yes
Aligner Clip Paired End Reads Overhang	aligner_clip_pe_overhang	Mapper	0,1,2	0	Yes
Enable Map Align	enable_map_align	Mapper	true / false	true	Yes
SV Somatic Hotspot BED File	sv_somatic_ins_tandup_hotspot_regions_bed	Structural VC	file	included	Yes
SV Systematic Noise File	sv_systematic_noise	Structural VC	file	included	Yes
Output SNV Evidence BAM	vc_output_evidence_bam	Debug	true / false	false	Yes
QC Detect Contamination	qc_detect_contamination	QC	true / false	true	Yes

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ℹ️ Note: For CRAM Input Reference Genome, a list of commonly-used human reference FASTA files can be downloaded from the Illumina support site:Illumina DRAGEN Product Files