🧬 Routine WGS QC and Assembly Workflow

This repository contains a Jupyter Notebook workflow for performing Quality Control (QC) and Genome Assembly
of bacterial Whole Genome Sequencing (WGS) data on the local sequencing server.

The notebook automates the standard GHRU workflow, combining:

• BactScout for QC
• GHRU-Assembly for genome assembly

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📋 Features

• ✅ Automatic setup of directory structure for each sequencing run
• ✅ Quality Control using BactScout (with Pixi environment)
• ✅ Manual QC interpretation step (final_summary.csv)
• ✅ Automatic generation of sample sheet for passed samples
• ✅ De novo genome assembly using GHRU-Assembly (Nextflow pipeline)
• ✅ Optional cleanup of work and .nextflow.log files
• ✅ Reproducible and auditable workflow with clear logs

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⚙️ Setup Instructions

1. Clone the Pipelines

mkdir -p /data/nihr/nextflow_pipelines/
cd /data/nihr/nextflow_pipelines/

# Clone BactScout and GHRU-Assembly
git clone https://github.com/ghruproject/bactscout.git
git clone https://github.com/ghruproject/GHRU-assembly.git

2. Create Conda Environments

# Create environment for BactScout (Pixi)
mamba create -n pixi python=3.10 -y
mamba run -n pixi pip install pixi

# Create environment for Nextflow (Assembly)
mamba create -n nextflow python=3.10 -y
mamba run -n nextflow mamba install -c bioconda nextflow -y

🧪 Running the Notebook

1. Launch JupyterLab or Jupyter Notebook on the sequencing server.
2. Open the notebook Routine_WGS_QC_and_Assembly.ipynb.
3. Update the base_dir variable to your current run folder (for example:
   /data/nihr/ghru2/2025/2025-09-22).
4. Run the cells sequentially from top to bottom.

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🧾 Workflow Summary

Step 1 – Define Run Folders

• Set up input_dir, output_dir, qc_dir, and assembly_dir.

Step 2 – Run QC (BactScout)

• Runs QC inside the Pixi environment.
• Generates final_summary.csv and multiqc_report.html.

Step 3 – Manual QC Review

• Open final_summary.csv and add a new column overall_status (PASSED or FAILED).

Step 4 – Generate Samplesheet

• Runs a script to create samplesheet_passed.csv containing only PASSED samples.

Step 5 – Run Assembly (GHRU-Assembly)

• Runs the Nextflow assembly pipeline inside the nextflow environment.
• Generates the assembly output and summary files.

Step 6 – Optional Cleanup

• Removes work/ and .nextflow.log files after successful completion.

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🧠 Notes

• Always verify QC results before running the assembly pipeline.
• You can modify the BactScout config file to include additional organisms if needed.
• Run cleanup only after confirming assembly completion.
• The notebook follows a fixed folder structure — avoid renaming or moving directories manually.

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🧑‍💻 Author

Varun Shamanna
Senior Bioinformatician, Central Research Laboratory, KIMS, Bengaluru
PhD Researcher