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
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 joincustomResourceDir
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
solid_custom_param.config
Content
solid_custom_param.config
Contentcustom_resources_solid_dir
Folder Structure
custom_resources_solid_dir
Folder StructurecustomConfig
Template (with default value)
customConfig
Template (with default value)Supported Parameters
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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