Welcome to this PoC demonstrating (one of the many) usecases of Nextflow in bioinformatics

Docs

This PoC is a mini bioinformatics pipeline with three steps:

• QC (Quality Check)
  Takes your FASTQ file (sequencing reads).
  Runs fastqc to check read quality.
  Produces a simple qc_report.html.

• ALIGN (Read Mapping)
  Takes your reads and the reference genome (reference.fa).
  Runs bwa mem to map reads onto the reference.
  Produces an aligned.bam file (where each read aligns on the genome).

• VARIANT_CALL (Variant Detection)
  Takes the alignment (aligned.bam) and reference.
  Uses samtools + bcftools to look for differences (mutations/variants) between your reads and the reference.
  Produces a variants.vcf file.

In super simple words:

• Step 1: “Are my DNA reads good?”
• Step 2: “Where do my reads fit in the reference genome?”
• Step 3: “What genetic changes do my reads have compared to the reference?”

How to run this project?

This PoC requires Linux (wsl has been used)

Set-Up

• Step 1. Install Java

1. Install Java (version >= 17)

sdk install java 17.0.10-tem

2. Confirm installation

java -version

• Step 2: Install Nextflow

1. Download Nextflow

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

2. Make Nextflow executable

chmod +x nextflow

3. Move Nextflow into an executable path. For example:

mkdir -p $HOME/.local/bin/
mv nextflow $HOME/.local/bin/

4. Confirm Nextflow is installed correctly

nextflow info

Running the project

• Step 1: Install the required dependencies/libraries/tools

sudo apt update
sudo apt install -y fastqc bwa samtools bcftools

• Step 2: Index the hoax chromosome file (reference.fa)

bwa index data/reference.fa

• Step 3: Run the pipeline

nextflow run main.nf

Expected outputs

Expected outputs in results/:
qc_report.html → FastQC report.
aligned.bam → aligned reads.
variants.vcf → called variants.