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 section of documentation typically contains an overview of the workflow in terms of motivation and bioinformatics methods, listing any key tools or algorithms employed, whilst also describing its range of use-cases and what a suitable input dataset should look like.
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 Singularity to provide isolation of the required software. Both methods are automated out-of-the-box provided either Docker or Singularity 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-template --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.
See Quality Control Workflow for the live QC report. See Differential Expression Workflow for cumulative BAM quantification and per-batch edgeR, fry, and GSVA refreshes. Differential expression and gene-set enrichment can be disabled independently; gene-set enrichment requires differential expression. QC-only runs do not require reference files, and differential-only runs do not require a GMT file.