Aggregate SuSiE Workflow

Pipeline Version	Date Updated	Documentation Author	Questions or Feedback
aou_9.0.2	January, 2026	WARP Pipelines	File an issue

Introduction to the Aggregate SuSiE workflow

AggregateSusieWorkflow.wdl merges per-phenotype SuSiE outputs and annotates the merged result with external reference resources.

It first aggregates all SuSiE parquet paths from a file-of-paths input, then annotates merged results using Gencode, allele-frequency, and functional annotation resources.

Inputs

Input descriptions

Input variable name	Description	Type
SusieParquetsFOFN	File-of-file-paths listing SuSiE parquet outputs to aggregate.	File
Memory	Runtime memory (GB).	Int
OutputPrefix	Prefix used for merged outputs.	String
NumThreads	CPU thread count for aggregation task.	Int
GencodeGTF	Gencode GTF for annotation context.	File
PlinkAfreq	Allele frequency table from PLINK processing.	File
AnnotationPhyloP	PhyloP annotation resource.	File
AnnotationENCODE	ENCODE cCRE annotation resource.	File
AnnotationFANTOM5	FANTOM5 annotation resource.	File
AnnotationVEP	VEP annotation table.	File
AnnotationGnomad	gnomAD annotation resource.	File
AnnotationVEPIndex	Index for VEP annotation table.	File

Outputs

Output variable name	Filename, if applicable	Output format and description
AnnotatedMergedSusieParquet	<OutputPrefix>_SusieMerged.annotated.tsv	Annotated merged SuSiE output table.

Workflow and WDL

• Workflow: AggregateSusieWorkflow
• Source WDL: AggregateSusieWorkflow.wdl

Versioning

All AggregateSusieWorkflow releases are documented in the changelog.

Feedback

Please help us make our tools better by filing an issue in WARP; we welcome pipeline-related suggestions or questions.