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 (http://www.nextflow.io) pipeline targeted for curation with nf-core (https://nf-co.re/). 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