HLA Make Table
| Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
|---|---|---|---|
| aou_9.0.0 | August, 2025 | WARP Pipelines | File an issue |
Introduction to the HLA Make Table workflow
MakeTable aggregates per-sample HLA consensus call files into a cohort-level summary table.
It verifies header consistency across samples and emits a unified matrix where each row corresponds to a sample and each gene is represented by two allele columns.
Quickstart table
| Pipeline Feature | Description | Source |
|---|---|---|
| Analysis type | Cohort-level HLA consensus aggregation | |
| Workflow language | WDL 1.0 | openWDL |
| Data input file format | Array of per-sample consensus text files + sample IDs | |
| Data output file format | Tab-delimited summary table | |
| Primary software | Bash text processing |
Set-up
HLA Make Table installation and requirements
The workflow code can be downloaded by cloning the WARP GitHub repository. For the latest release, please see the MakeTable changelog.
The pipeline can be deployed using Cromwell, a GA4GH-compliant workflow management system.
Inputs
Input descriptions
| Input variable name | Description | Type |
|---|---|---|
consensus_calls | Ordered array of per-sample HLA consensus files. | Array[File] |
sample_ids | Ordered array of sample IDs aligned to consensus_calls. | Array[String] |
HLA Make Table tasks and tools
This workflow runs a single task to combine sample files.
| Task name and WDL link | Tool | Software | Description |
|---|---|---|---|
| Combine | shell text processing | continuumio/anaconda:latest | Builds a shared header, verifies consistency, and writes cohort-wide result table. |
1. Combine per-sample consensus files
Combine iterates through consensus files, builds/compares gene headers, appends genotype rows, and prepends sample IDs to create the final output matrix.
Outputs
| Output variable name | Filename, if applicable | Output format and description |
|---|---|---|
result | result.txt | Cohort-level HLA summary table with sample IDs and diploid allele columns per gene. |
Versioning
All MakeTable 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.