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Workflow template

This repository contains a nextflow workflow template that can be used as the basis for creating new workflows.

This workflow is not intended to be used by end users.


This workflow provides a simple way to analyse Monkeypox sequencing data; taking raw Oxford Nanopore Technologies reads and creating a draft consensus and assembly. No trimming of sequences is carried out so be vigilant when using targeted data.


The workflow uses nextflow to manage compute and software resources, as such nextflow will need to be installed before attempting to run the workflow.

The workflow can currently be run using either Docker or conda to provide isolation of the required software. Both methods are automated out-of-the-box provided either docker of conda is installed.

It is not required to clone or download the git repository in order to run the workflow. For more information on running EPI2ME Labs workflows visit out website.

Workflow options

To obtain the workflow, having installed nextflow, users can run:

nextflow run epi2me-labs/wf-mpx --help

to see the options for the workflow.

Workflow outputs

The primary outputs of the workflow include:

  • a simple text file providing a summary of sequencing reads,
  • an HTML report document detailing the primary findings of the workflow.
  • a draft consensus sequence obtained
  • a medaka polished assembly

Useful links