This repository contains a simple, modular Nextflow pipeline that performs quality trimming of FASTQ files using Unix tools (e.g., cutadapt) and sequence alignment using bowtie2. The project demonstrates how to build reproducible, automated workflows for NGS data processing using Nextflow.
- Automatic detection of FASTQ input files
- Trimming & filtering of sequencing reads using
cutadapt - Reference genome indexing using
bowtie2-build - Sequence alignment using
bowtie2. - Output generation in trimmed FASTQ and SAM formats
- Fully reproducible Nextflow workflow
This project was created to:
- Practice writing modular Nextflow pipelines.
- Understand processes, channels, inputs, and outputs.
- Learn how to integrate common NGS tools in a workflow
- Demonstrate FASTQ trimming and basic read alignment
- It serves as a foundational template for beginners learning workflow automation in bioinformatics.
