https://github.com/kgorze/rna-seq-nextflow

A reproducible, scalable, and containerized RNA-Seq analysis pipeline implemented in Nextflow. Features modular design with quality control (FastQC/MultiQC), alignment (STAR/HISAT2), quantification (Salmon/featureCounts), and differential expression analysis (DESeq2) components. Includes Docker containerization and CI/CD with GitHub Actions.
https://github.com/kgorze/rna-seq-nextflow

bioinformatics differential-expression docker nextflow pipeline rna-seq

Last synced: 4 months ago
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A reproducible, scalable, and containerized RNA-Seq analysis pipeline implemented in Nextflow. Features modular design with quality control (FastQC/MultiQC), alignment (STAR/HISAT2), quantification (Salmon/featureCounts), and differential expression analysis (DESeq2) components. Includes Docker containerization and CI/CD with GitHub Actions.

• Host: GitHub
• URL: https://github.com/kgorze/rna-seq-nextflow
• Owner: kGorze
• Created: 2025-04-07T15:44:02.000Z (about 1 year ago)
• Default Branch: main
• Last Pushed: 2025-04-08T19:56:24.000Z (about 1 year ago)
• Last Synced: 2025-04-14T12:09:16.369Z (about 1 year ago)
• Topics: bioinformatics, differential-expression, docker, nextflow, pipeline, rna-seq
• Language: HTML
• Homepage:
• Size: 8.63 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 4
• Metadata Files:
  • Readme: README.md

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README

          
# RNA-Seq Nextflow Pipeline

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

![image](https://github.com/user-attachments/assets/610a28da-9498-4bcb-aa79-8f7948121221)

## Quick start

```bash

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](https://github.com/kGorze/RNA-Seq-Nextflow)