Demo of a Nextflow Pipeline for bulk-RNA Seq
Note: This pipeline is designed to be a demo to learn how to construct as well as run a nextflow pipeline.
This pipeline manages a RNA-Seq workflow starting from raw fastq files and converting them to standard file formats for use by downstream tools. The steps involved are:
- FastQC: Import of data from BAM, SAM or FastQ files (any variant). This tool provides a quick overview to tell you in which areas there may be problems. Creates a summary graphs and tables to quickly assess your data.
- Trim Galore: Adapter Trimming
- STAR: Alignment of reads to reference genome.
This repository uses Nextflow for pipeline managment, Conda for Environment Management, FastQC, STAR, and TrimGalore.
We have handled all software requirements using Conda.
The only thing user will need to install is miniconda, which can be installed following this manual:
https://educe-ubc.github.io/conda.html
Clone this repo:
git clone https://github.com/bwh-bioinformatics-hub/nextflow_demo.git
Once you have cloned the repo, to create conda environment with dependencies installed
conda env create -f env/environment.yml
Once the Conda environment has been installed to run:
nextflow run rna_seq_pipeline.nf with-conda ~/miniconda3/envs/rna_seq_pipeline