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2.nf core Applications

What is nf-core?

nf-core is a community effort to generate a curated set of standardized, reproducible, documented, NGS analysis pipelines. All these workflows are built using the versitile workflow manager, Nextflow.

This process has resulted in workflows that all have the following characteristics:

  • Integrated software dependency management (Docker, Singularity, Conda).
  • Portability to run your pipelines anywhere: laptop, cluster, or cloud.
  • Reproducibility of analyses independent of time and computing platform.

Eventhough these pipelines have been build to be user-friendly they are nonetheless complilcated pieces of software which, for effective use, typically require:

  • Access to and familiarity with the Unix computer archiceture and file systems
  • An understanding of the concepts of containers (Docker/Singularity/conda)
  • Familiarity with the steps involved in the analysis of a given experimental protocal (e.g. RNASEQ).
  • Access to the appropriate Genome Data (sequences and annotations) for the desired genome version.

nf-core on DNAnexus

As mentioned above, nf-core pipelines in their native format, present some challenges for those who are not "professional bioinformatitians". To facilitiate the use of these pipelines by the less skilled users the Genome Analysis Unit has implement the most common nf-core pipelines within the DNAnexxus Cloud environment. (CBAP) This implementation offers several advantages.

  • A simple to use Grapical User Interface (GUI)... point and click
  • Ready access to a Cloud network of computation resource for faster execution via distributed network of processing power.
  • Integrated documantatin offering A guided approach to each analysis

GAU has also taken the approach of presenting each of thses workflows in two formats:

  1. The simplified interface - Offering a pared down set of user choices, guided selection of available genomes (organism and version), simpolified input and enhanced output.
  2. The full interface - for sophisticated users who want to access the full set of choices availavle with the workflow, this version present the native workflwo with all its options, available via either the DNAnexus GUI or CLI interface. 4.