Nextflow Pipeline for Genomic Data QC and MultiQC Reporting

Overview

This pipeline is designed to download .fastq.gz files from a Synapse repository, run quality control (QC) using FastQC, and generate a combined report using MultiQC. The workflow is implemented using Nextflow for easy reproducibility and extensibility.

Requirements

• Nextflow: Version 24.04.3 or later. Install from nextflow.io.
• Java: Required for running Nextflow.
• Python: Python 3.x must be installed.
• SynapseClient: Install using pip install synapseclient.
• FastQC and MultiQC: Ensure these tools are installed and available in your PATH, or use containers.

Alternatively, you can use the provided install_dependencies.sh script to install all necessary dependencies:

./install_dependencies.sh

Installation

1. Clone this repository:

   git clone https://github.com/yourusername/project.git
   cd project

2. Ensure dependencies are installed:

   pip install synapseclient

3. Log in to Synapse:

   • Use synapse login or ensure you have a .synapseConfig file set up in your home directory.

Running the Pipeline

Run the pipeline with a specified Synapse ID:

nextflow run main.nf --synapse_id <your_synapse_id>

Parameters

• --synapse_id: The Synapse ID of the data folder or file containing .fastq.gz files (e.g., syn22093319).

Testing Instructions

To test the workflow, you can use the folder syn64097744 as the test folder. The files required for testing are also included in this folder.

To run the test, use the following command:

nextflow run main.nf --synapse_id syn64097744

This command will execute the workflow using the provided test folder and its contents.

Workflow Steps

1. Download Data: Data is downloaded from Synapse using the given Synapse ID.
2. Run FastQC: Each .fastq.gz file is processed using FastQC to generate quality control metrics.
3. Run MultiQC: The outputs from all FastQC runs are aggregated into a single report using MultiQC.

Output

• FastQC Results: Individual FastQC result files are stored in the results/fastqc/ directory.
• MultiQC Report: The pipeline generates a multiqc_report.html file that combines all the QC outputs in a single report, saved in the results/ directory.

Folder Structure

• results/: Directory where the quality control reports will be generated after running the workflow.

Troubleshooting

• Ensure Synapse authentication is set up properly.
• Verify that FastQC and MultiQC are installed or available in your container.

License

This project is licensed under the MIT License.