This pipeline is currenlty under development. The workflow is not yet finished.

nf-core/cageseq is a pipeline built for the analysis of CAGE-sequencing data.

Analysis steps consist of adapter and artefact trimming (cuatadapt), alignment to a reference (STAR) and CAGE tag counting. Additionally, several quality control steps (FastQC, MultiQC) are included to allow for easy verification of results after a run.

The pipeline is built using Nextflow, a 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.

Currently, this pipeline only supports CAGE-seq data generated with the old protocol as desribed in CAGE-seq. The recently developed new CAGE-seq protocol will however be implemented in future releases.


The nf-core/cageseq pipeline comes with documentation about the pipeline, found in the docs/ directory:

  1. Installation
  2. Pipeline configuration
  3. Running the pipeline
  4. Output and how to interpret the results
  5. Troubleshooting


nf-core/cageseq was originally written by Kevin Menden and Tristan Kast.