🔄 WDL to CWL Converter

This Python tool converts WDL (Workflow Description Language) files into CWL (Common Workflow Language) format. It supports task-only WDLs, full workflow definitions, and import statements from external files.

Tested using:

• Broad Institute's Illumina Genotyping Array WDLs
• Seven Bridges' CAVATICA platform CWL workflows

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✅ Features

• ✅ Converts individual WDL task blocks into CWL CommandLineTool definitions
• ✅ Converts full workflow blocks into CWL Workflow definitions
• ✅ Resolves local WDL import statements and rewrites them as .cwl dependencies
• ✅ Preserves runtime information such as dockerPull
• ✅ Handles Broad-style WDLs with optional/default inputs

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📦 Requirements

Python 3.7 or later

Install dependencies with:

pip install -r requirements.txt

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⚠️ Important Notes on Execution

This converter focuses on translating WDL structure into CWL-compatible definitions, but it does not guarantee a fully executable pipeline out of the box.

If your WDL workflow imports tasks (e.g., Broad's IlluminaGenotypingArray workflow), you must:

✅ Convert each imported WDL file (e.g., IlluminaGenotypingArrayTasks.wdl, Qc.wdl) to CWL separately

✅ Ensure all converted .cwl tool files are present in the same directory as the main workflow CWL

⚠️ CWL does not support if, scatter, or dynamic expressions exactly as WDL does. These constructs may be skipped or simplified in conversion.

🔧 You may need to manually adjust input wiring, runtime options, or expression logic for full compatibility

This tool is best used as a starting scaffold to help wrap existing WDL pipelines into CWL format. Final validation and polish is expected before production use.

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How It Works

• parse_wdl() uses miniwdl to load WDL files and resolve any imports
• convert_task_to_cwl() converts each task block into a valid CWL CommandLineTool
• convert_workflow_to_cwl() builds a CWL Workflow from the workflow block, generating steps and input mappings
• If a WDL has only tasks and no workflow, the script outputs one CWL file per task

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🛠️ Usage

python3 wdl_to_cwl.py <main_wdl_file> <output_cwl_file> [--import-dir <path_to_imports>]

Examples

Convert a full workflow with local imports: python3 wdl_to_cwl.py IlluminaGenotypingArray.wdl broad_IlluminaGenotypingArray.cwl --import-dir ./tasks/

Convert a task-only WDL:

python3 wdl_to_cwl.py Qc.wdl broad_QC.cwl

If the WDL contains only tasks, each task is saved as its own CWL file:

broad_QC_task0.cwl broad_QC_task1.cwl ...

📁 Output Structure

WDL Input Type	Output Type	Notes
workflow	Single CWL Workflow file	Tasks must be imported separately as .cwl
task-only WDL	Separate CWL per task	No workflow {} block required

Contact

Feel free to fork, submit issues, or contribute to the project.

Author: Phillip Webster