*nfcore/rnaseq* is a bioinformatics analysis pipeline used for RNA sequencing data.

The workflow processes raw data from FastQ inputs (FastQC, Trim Galore!), aligns the reads (STAR or HiSAT2), generates gene counts (featureCounts, StringTie) and performs extensive quality-control on the results (RSeQC, dupRadar, Preseq, edgeR, MultiQC). See the output documentation for more details of the results.

The pipeline is built using Nextflow, a bioinformatics workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.


The nfcore/rnaseq pipeline comes with documentation about the pipeline, found in the docs/ directory:

  1. Installation
  2. Pipeline configuration
    * Local installation
    * Amazon Web Services (aws)
    * Swedish UPPMAX clusters
    * Swedish cs3e Hebbe cluster
    * Tübingen QBiC
    * CCGA Kiel
    * Adding your own system
  3. Running the pipeline
  4. Output and how to interpret the results
  5. Troubleshooting


These scripts were originally written for use at the National Genomics Infrastructure, part of SciLifeLab in Stockholm, Sweden, by Phil Ewels (@ewels) and Rickard Hammarén (@Hammarn).

Many thanks to other who have helped out along the way too, including (but not limited to):