47 lines
1.4 KiB
Markdown
47 lines
1.4 KiB
Markdown
# Workflow template
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This repository contains a [nextflow](https://www.nextflow.io/) workflow
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template that can be used as the basis for creating new workflows.
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> This workflow is not intended to be used by end users.
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## Quickstart
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The workflow uses [nextflow](https://www.nextflow.io/) to manage compute and
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software resources, as such nextflow will need to be installed before attempting
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to run the workflow.
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The workflow can currently be run using either
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[Docker](https://www.docker.com/products/docker-desktop) or
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[conda](https://docs.conda.io/en/latest/miniconda.html) to provide isolation of
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the required software. Both methods are automated out-of-the-box provided
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either docker of conda is installed.
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It is not required to clone or download the git repository in order to run the workflow.
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For more information on running EPI2ME Labs workflows [visit out website](https://labs.epi2me.io/wfindex).
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**Workflow options**
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To obtain the workflow, having installed `nextflow`, users can run:
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```
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nextflow run epi2me-labs/wf-template --help
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```
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to see the options for the workflow.
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**Workflow outputs**
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The primary outputs of the workflow include:
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* a simple text file providing a summary of sequencing reads,
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* an HTML report document detailing the primary findings of the workflow.
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## Useful links
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* [nextflow](https://www.nextflow.io/)
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* [docker](https://www.docker.com/products/docker-desktop)
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* [conda](https://docs.conda.io/en/latest/miniconda.html)
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