RNA-Seq Nextflow Pipeline

A reproducible, containerized RNA‑seq workflow from FASTQ to differential expression implemented in Nextflow.

Quick start

git clone https://github.com/kGorze/RNA-Seq-Nextflow
cd RNA-Seq-Nextflow
nextflow run main.nf -profile test,docker

# run on your data
nextflow run main.nf -profile docker \
  --reads 'reads/*_R{1,2}.fastq.gz' \
  --genome genome.fa --gtf genes.gtf \
  --outdir results

Minimal parameters

flag	meaning
--reads	Paired FASTQ glob (*_R{1,2}.fastq.gz)
--genome	Reference genome FASTA
--gtf	Gene annotation GTF
--design	Sample design CSV for DESeq2 (optional)

Full list: docs/parameters.md.

Profiles

• docker / singularity – containerised (default docker)
• test – tiny dataset for CI / validation
• slurm / sge / standard – customise for your cluster / local install

Combine with commas: -profile test,docker.

Outputs (key files)

path	content
01_quality_control/multiqc_report.html	QC summary
03_alignment/*/Log.final.out	Alignment stats
04_quantification/merged_gene_counts.csv	Gene counts
05_differential_expression/deseq2/*.csv	DE results
06_reports/final_report.html	End‑to‑end report

Cite

Gorzelanczyk K. (2025) Reproducible RNA‑Seq analysis with Nextflow. https://github.com/kGorze/RNA-Seq-Nextflow