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.

Work in progress - this is a community effort in building a pipeline capable to support:

  • Alevin + AlevinQC
  • STARSolo
  • Kallisto + BUStools


The nf-core/scrnaseq 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


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).


You can cite the nf-core pre-print as follows:
Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. nf-core: Community curated bioinformatics pipelines. bioRxiv. 2019. p. 610741. doi: 10.1101/610741.

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.