phyloTreeViz-WDL

A WDL workflow for automated rendering of phylogenetic trees from Newick files using ETE3, supporting customizable image format, font size & resolution in a reproducible Docker environment.

Phylogenetic tree visualization workflow using WDL & ETE3

This WDL-based workflow renders phylogenetic trees from Newick format files using the powerful ETE3 Python library. It supports rendering multiple trees in parallel, with customizable font size, width & image format.

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Features

• Supports batch rendering of .nwk Newick files
• Generates high-resolution tree images (PNG, SVG)
• Customizable width & font size
• Clean render logs for debugging
• Dockerized for reproducibility

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Requirements

• Cromwell
• Docker (or Singularity for HPC environments)
• WDL 1.0 compatible runner
• Input Newick trees

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Quickstart

1. Clone this repository

git clone https://github.com/gmboowa/phyloTreeViz-WDL.git
cd phyloTreeViz-WDL

2. Prepare input JSON

{
  "TREE_VISUALIZATION.input_trees": [
    "~/core_core_genes.nwk",
    "~/accessory_accessory_genes.nwk"
  ],
  "TREE_VISUALIZATION.width": 1200,
  "TREE_VISUALIZATION.image_format": "png",
  "TREE_VISUALIZATION.font_size": 8
}

3. Run the workflow with Cromwell

java -jar cromwell.jar run phyloTreeViz-WDL.wdl -i inputs.json

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Output

Each tree will result in:

• A rendered image (phylogenetic_tree_<input>.png)
• A detailed log file (render_<input>.log)

They will be found in the final_phylogenetic_tree_image/ directory per task.

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Docker image

The workflow uses the pre-built Docker image:

gmboowa/ete3-render:1.14

This image comes with:

• Python 3
• ETE3
• All dependencies pre-installed

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Repository structure

.
├── workflows/
│   └── TREE_VISUALIZATION.wdl         # Main WDL workflow
├── inputs/
│   └── example_inputs.json            # Example JSON input
├── test_data/
│   ├── core_core_genes.nwk            # Sample Newick trees
│   └── accessory_accessory_genes.nwk
├── docker/

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License

MIT License – see LICENSE file for details.

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Acknowledgments

Uses ETE3 for tree rendering.

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Troubleshooting

• Missing Docker? Ensure Docker is installed and accessible to Cromwell.
• Tree not rendered? Check logs in render_*.log for Python errors.
• No output image? Ensure input .nwk file is valid and has correct format.

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Contact

For questions, suggestions, or contributions, feel free to open an issue or pull request.