{"id":27425617,"url":"https://github.com/kgorze/rna-seq-nextflow","last_synced_at":"2026-01-24T15:07:23.490Z","repository":{"id":286687748,"uuid":"962067829","full_name":"kGorze/RNA-Seq-Nextflow","owner":"kGorze","description":"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. 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Nextflow.\n![image](https://github.com/user-attachments/assets/610a28da-9498-4bcb-aa79-8f7948121221)\n\n\n## Quick start\n\n```bash\ngit clone https://github.com/kGorze/RNA-Seq-Nextflow\ncd RNA-Seq-Nextflow\nnextflow run main.nf -profile test,docker\n\n# run on your data\nnextflow run main.nf -profile docker \\\n  --reads 'reads/*_R{1,2}.fastq.gz' \\\n  --genome genome.fa --gtf genes.gtf \\\n  --outdir results\n```\n\n## Minimal parameters\n\n| flag       | meaning                                 |\n| ---------- | --------------------------------------- |\n| `--reads`  | Paired FASTQ glob (`*_R{1,2}.fastq.gz`) |\n| `--genome` | Reference genome FASTA                  |\n| `--gtf`    | Gene annotation GTF                     |\n| `--design` | Sample design CSV for DESeq2 (optional) |\n\nFull list: `docs/parameters.md`.\n\n## Profiles\n\n* **docker** / **singularity** – containerised (default docker)\n* **test** – tiny dataset for CI / validation\n* **slurm** / **sge** / **standard** – customise for your cluster / local install\n\nCombine with commas: `-profile test,docker`.\n\n## Outputs (key files)\n\n| path                                       | content           |\n| ------------------------------------------ | ----------------- |\n| `01_quality_control/multiqc_report.html`   | QC summary        |\n| `03_alignment/*/Log.final.out`             | Alignment stats   |\n| `04_quantification/merged_gene_counts.csv` | Gene counts       |\n| `05_differential_expression/deseq2/*.csv`  | DE results        |\n| `06_reports/final_report.html`             | End‑to‑end report |\n\n\n## Cite\n\n\u003e Gorzelanczyk K. (2025) Reproducible RNA‑Seq analysis with Nextflow. [https://github.com/kGorze/RNA-Seq-Nextflow](https://github.com/kGorze/RNA-Seq-Nextflow)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkgorze%2Frna-seq-nextflow","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkgorze%2Frna-seq-nextflow","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkgorze%2Frna-seq-nextflow/lists"}