RNA-seq AoU Processing

Pipeline Version	Date Updated	Documentation Author	Questions or Feedback
aou_9.0.1	June, 2025	WARP Pipelines	File an issue

Introduction to the RNA-seq AoU Processing workflow

rnaseq_aou.wdl defines workflow rnaseq_pipeline_bam_workflow, which orchestrates GTEx-style RNA-seq processing from aligned reads through expression quantification and QC task chains.

It calls samtofastq, star, rsem, markduplicates, and rnaseqc2 component WDLs to produce alignment/quantification artifacts used in downstream eQTL/sQTL workflows.

Quickstart table

Pipeline Feature	Description	Source
Analysis type	RNA alignment and quantification orchestration
Workflow language	WDL 1.0	openWDL
Data input file format	task-level inputs provided through imported component workflows
Data output file format	task-level outputs from STAR/RSEM/RNA-SeQC components
Primary software	STAR, RSEM, RNA-SeQC (via imported WDLs)

Set-up

RNA-seq AoU Processing installation and requirements

The workflow code can be downloaded by cloning the WARP GitHub repository. For the latest release, please see the rnaseq_aou changelog.

The pipeline can be deployed using Cromwell, a GA4GH-compliant workflow management system.

Inputs

Input descriptions

Input variable name	Description	Type
prefix	Prefix passed to component RNA-seq tasks for naming and sample identity propagation.	String

RNA-seq AoU Processing tasks and tools

This workflow is an orchestration wrapper around imported GTEx-derived WDLs.

1. Convert alignment to FASTQ
2. Align and quantify transcripts
3. Mark duplicates and run RNA QC

Task name and WDL link	Tool	Software	Description
samtofastq	imported task	see samtofastq.wdl	Generates FASTQ from input alignment.
star	imported task	see star.wdl	Performs STAR alignment.
rsem	imported task	see rsem.wdl	Generates expression quantification outputs.
markduplicates	imported task	see markduplicates.wdl	Marks duplicate reads in aligned BAM.
rnaseqc2	imported task	see rnaseqc2.wdl	Produces RNA quality metrics.

1. Convert alignment to FASTQ

samtofastq emits paired FASTQs for downstream alignment.

2. Align and quantify transcripts

star and rsem generate alignments and expression quantifications.

3. Mark duplicates and run RNA QC

markduplicates and rnaseqc2 produce cleaned BAMs and QC outputs used by downstream analyses.

Outputs

This wrapper workflow does not declare a top-level output block in the WDL. Outputs are available from called component tasks in execution metadata.

Versioning

All rnaseq_aou 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.