VariantFlow

End-to-end WGS analysis pipeline using Nextflow DSL2 and GATK best practices. Performs QC, alignment, variant calling, filtering, annotation, and downstream analysis. Designed for reproducible, scalable genomics workflows on HPC and cloud environments with publication-ready outputs.

Pipeline Summary

1. FASTQC - Raw read quality control.
2. ALIGN - Read alignment to reference genome using BWA.
3. BAM_PROCESS - Sorting, marking duplicates, and indexing using Samtools and GATK.
4. VARIANT_CALLING - Per-sample variant calling using GATK HaplotypeCaller (GVCF mode).
5. JOINT_GENOTYPING - Cohort-level joint genotyping using GATK CombineGVCFs and GenotypeGVCFs.
6. ANNOTATION - Variant annotation using Ensembl VEP.

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Requirements

To run this pipeline, you will need:

1. Nextflow (>= 22.04)
2. Conda (Miniconda or Anaconda) - Nextflow will automatically build the required environment using the provided environment.yml.

Quick Start (Test Run)

This pipeline includes a built-in test profile with tiny dummy files to verify the pipeline works on your machine.

1. Clone the repository

git clone https://github.com/Mkddb/VariantFlow.git
cd VariantFlow

2. Run a Stub Test (Fast - No tools required)

This tests the Nextflow logic and file-flow without running heavy bioinformatics tools or requiring large VEP caches.

nextflow run main.nf -profile test -stub-run

3. Run the Full Test (Requires Conda)

This runs the actual bioinformatics tools (GATK, Samtools, VEP, etc.) on the tiny test data. Nextflow will automatically create a Conda environment for you, which may take a few minutes the first time.

nextflow run main.nf -profile test -resume

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Running on Real Data

To run the pipeline on your own data, you can override the default parameters via the command line.

nextflow run main.nf \
   -profile standard \
   --reads "/path/to/your/data/*_{1,2}.fastq.gz" \
   --genome "/path/to/your/reference.fa" \
   --outdir "my_results" \
   --vep_cache "/path/to/your/vep_cache"

Core Parameters

Parameter	Description	Default
--reads	Path to paired-end FASTQ files (glob pattern)	data/test/*_{1,2}.fastq.gz
--genome	Path to the reference genome FASTA file	assets/reference.fa
--outdir	Directory where results will be saved	results
--vep_cache	Path to the Ensembl VEP cache directory	${projectDir}/vep_cache
--interval	Interval (BED) file for targeted regions (opt)	null

Directory Structure

VariantFlow/
├── main.nf              # Main workflow script
├── nextflow.config      # Pipeline configuration (profiles, resources)
├── environment.yml      # Conda environment recipe
├── assets/              # Reference genomes and indices
├── bin/                 # Custom helper scripts (e.g., summary.py)
├── data/                # Test data
├── modules/             # Nextflow DSL2 process modules
└── expected/            # Expected output for testing

License

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