Chapter 2 nf-core/scflow

2.0.1 About nf-core/scflow

The nfcore/scflow pipeline enables fully automated, reproducible analyses of single-cell data at scale in the Cloud (GCP/AWS), in a high-performance computing (HPC) environment, or on a local workstation using the scFlow toolkit.

nf-core/scflow is a NextFlow ( pipeline targeted for curation with nf-core ( Key features include: -

  • Single-line execution of a complete analysis following best-practices

  • Analytical steps are parallelized and distributed efficiently at scale on a High Performance Computing (HPC) environment, in the Cloud (e.g. GCP, AWS), or on a local workstation.

  • Smart cache allows parameters to be fine-tuned and analyses resumed

  • Input parameters are standardized and documented

  • The pipeline is version controlled for reproducibility

  • The analysis environment is provided by version controlled Docker/Singularity images

  • Pipeline outputs are standardized and include publication-quality plots, tables, and interactive reports