nf-run-snpAD

Overview

nf-run-snpAD is a Nextflow pipeline designed to run SNP analysis on BAM files. This pipeline processes samples with or without UDG treatment based on the provided input.

Prerequisites

Nextflow: Ensure you have Nextflow installed. You can install it by running:

curl -s https://get.nextflow.io | bash

• Java: Nextflow requires Java. Make sure you have Java (version 8 or higher) installed on your system.
• Modules: This pipeline includes several local modules that must be available in the designated paths.

Installation

Clone the repository or download the pipeline files:

git clone https://github.com/jbv2/run-snpAD.git
cd nf-run-snpAD

Usage

To run the pipeline, use the following command:

nextflow run main.nf -profile <profile_name> --input_tsv <path_to_input_tsv>

Parameters

--input_tsv: Path to the TSV file containing sample information (sample_id, inputbam, bai, udg). -profile: Specify a Nextflow profile (e.g., test, docker, etc.) for execution.

Input TSV Format Your input TSV file should have the following format:

sample_id	inputbam	bai	udg
sample1	sample1.bam	sample1.bai	true
sample2	sample2.bam	sample2.bai	false

Example Command

nextflow run main.nf -profile test --input_tsv test/data/test.tsv

Output

The pipeline generates the following outputs:

• VCF files containing the called variants for each sample, stored in the defined output directory.

Note

Ensure that your input files and paths are correctly set, and that you have the necessary permissions to read the files and write the outputs.

Support

For issues or questions, please open an issue on the GitHub repository.

License

This project is licensed under the MIT License - see the LICENSE file for details.