nf-core/scrnaseq is a bioinformatics best-practise analysis pipeline for

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 containers making installation trivial and results highly reproducible.

This is a community effort in building a pipeline capable to support:

  • Alevin + AlevinQC
  • STARSolo
  • Kallisto + BUStools

Pipeline Summary

By default, the pipeline currently performs the following:

  • Sequencing quality control (FastQC)
  • Overall pipeline run summaries (MultiQC)


The nf-core/scrnaseq pipeline comes with documentation about the pipeline: usage and output.


The nf-core/scrnaseq was initiated by Peter J. Bailey (Salmon Alevin, AlevinQC) with major contributions from Olga Botvinnik (STARsolo, Testdata) and Alex Peltzer (Kallisto/BusTools workflow).

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don’t hesitate to get in touch on the Slack #scrnaseq channel (you can join with this invite).


The basic benchmarks that were used as motivation for incorporating the three available modular workflows can be found in this publication.

We offer all three paths for the processing of scRNAseq data so it remains up to the user to decide which pipeline workflow is chosen for a particular analysis question.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.