MobiDL alignmentSR

WDL workflow for short-read alignment in capture-based panel sequencing.

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📌 Overview

WDL workflow for short-read alignment in capture-based panel sequencing. It is designed to be modular, reproducible, and optimized for use in clinical settings.

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🛠️ Requirements

Software Dependencies

• WDL (Workflow Description Language)
• Cromwell (Workflow Execution Engine)
• Apptainer (for containerized tools)

Apptainer images

This workflow is designed to be used on HPC cluster with apptainer images. You could install images from this repo : https://github.com/MobiDL/apptainer-recipes

Inputs

• FastQ files (paired-end)
• Reference genome (e.g., GRCh38)
• Target regions (BED file for panel definition)

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🚀 Quick Start

⚠️ For maximum compatibility across Cromwell and cluster backends, all input and output paths must be absolute paths.

1. Clone the Repository

git clone --recursive https://github.com/MobiDL/alignmentSR.git
cd alignmentSR

2. Backend Configuration

Before running the workflow, adapt the backend configuration to match your HPC environment.

Common parameters to review include:

• queue
• tmp_dir
• root_dir
• temporary-directory
• root

These parameters are usually cluster-specific and may need to be adjusted depending on your scheduler and storage architecture.

3. Run the Test Dataset

A minimal test dataset is available in the tests directory.

Update the paths in tests/test.json, then run:

java cromwell run alignmentSR.wdl \
  -Dconfig.file=backends.conf/slurm_apptainer.conf \
  -i tests/test.json

3. Configure Inputs

Edit the inputs.json file to specify your input files and parameters:

{
	"alignmentSR.sample": "SampleName",
	"alignmentSR.fasta": "/path/to/my/genomes/GRCh38/GRCh38.fa",
	"alignmentSR.fastq_R1": "/path/to/my/fastq_R1.fastq.gz",
	"alignmentSR.fastq_R2": "/path/to/my/fastq_R2.fastq.gz",
	"alignmentSR.knownSites": [
		"/path/to/my/knownsites_1.vcf.gz",
		"/path/to/my/knownsites_2.vcf.gz"
	],
	"alignmentSR.bed": "/path/to/my/intervals.bed",
	"alignmentSR.outputPath": "/path/to/my/output"
}

4. Run the Workflow

java cromwell run alignmentSR.wdl -Dconfig.file=backends.conf/slurm_apptainer.conf -i inputs.json

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📂 Repository Structure

alignmentSR/
├── backends.conf/           # Backends sub-repository
├── modules/                 # Modules sub-repository
├── tests/                   # tests directory containing minimal dataset
├── alignmentSR.wdl          # Main workflow file
├── inputs.json              # Example input configuration
└── README.md                # This file

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⚙️ Workflow Steps

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📊 Outputs

• BAM files: Aligned and processed reads.
• QC Reports: FastQC, MultiQC, and alignment metrics.
• Logs: Execution logs for debugging.

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🤝 Contributing

Contributions are welcome! Please open an issue or submit a pull request for any improvements or bug fixes.

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🆘 Support

For any questions or issues, please open an issue in this repository or contact us.