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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.

Requirements

  • Nextflow: Install from nextflow.io.
  • Python: Ensure Python 3.x is installed.
  • SynapseClient: Install using pip install synapseclient.
  • FastQC and MultiQC: Ensure these tools are installed and available in your PATH, or use containers if preferred.
  • Docker/Singularity (optional): To use containers for reproducibility.

Installation

  1. Clone this repository:

    git clone https://github.com/ncihtan/nf-htan-qc.git
cd project

  2. Ensure dependencies are installed:

    pip install synapseclient

  3. Log in to Synapse:

    • Ensure you are logged in using synapse login or have a .synapseConfig file set up in your home directory.

Running the Pipeline

Run the pipeline with a prepared sample sheet (csv):

nextflow run main.nf --input_csv /absolute/path/to/input.csv

Parameters

input_csv: Absolute path to the input CSV file. This file should have two columns:

  • filename: The exact name of the file to download (e.g., file1.fastq.gz).
  • synapse_id: The Synapse ID containing the file (e.g., syn12345678)

Output

  • The pipeline generates a multiqc_report.html file that combines all the QC outputs in a single report.
  • Individual FastQC result files are stored in the fastqc_results/ directory.

Notes

  • The pipeline only processes .fastq.gz files. Ensure your Synapse data folder contains these files.
  • If using Docker or Singularity, adjust the nextflow.config to include container paths.

Troubleshooting

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

Example Usage

Use input.csv' in /test to test the pipeline

nextflow run main.nf --input_csv /path/to/input.csv

This will download all .fastq.gz files from the specified Synapse ID, run QC on them, and produce a multiqc_report.html summarizing the QC results.