Nextflow Pipelines for Bioinformatics Analysis of Sequencing Data from Multiple Samples

Note: this repository will be continually updated as scripts are tested. Pipelines not ready for deployment are noted as in development below.

The main purpose of this repository is to share nextflow scripts that process sequencing data from multiple samples. These scripts have been designed for a specific purpose, such as trimming reads from multiple paired samples, and are an alternative to setting up bash loops or writing other custom scripts.

Setup

There are two ways to install the software needed to run the nextflow scripts. The recommended way is to set up a conda environment which will install all the software needed, including nextflow, to run a pipeline. Instructions for setting up conda environments are detailed in the documentation. An alternative is to install all the software needed manually and then call a nextflow script. If using this manual approach, the software dependencies for each pipeline is detailed in the documentation.

Conda or Mamba

Install conda from miniforge3 or from miniconda3.

Add conda channels:

conda config --add channels conda-forge
conda config --add channels bioconda

Clone Repository

Clone this repository to download the nextflow scripts (src) and the conda environment setup files (env) to the home directory:

cd $HOME
git clone https://github.com/Tom-Jenkins/nextflow-pipelines.git

Nextflow

If you are manually installing software, nextflow can be installed by following the installation docs. The scripts have currently been tested with nextflow v24.04.4 and java v18.0.2.1 2022-08-18.

Documentation

Nextflow Pipeline

• Trim paired-end reads
• Align paired-end reads to reference
• Organelle assembly and annotation
• Classify paired-end reads using Kraken2
• Variant Calling

In Development