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_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

## 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)

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