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Thomas Davis committed Jan 18, 2024
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Expand Up @@ -18,15 +18,14 @@ The pipeline performs epitope predictions for a given set of variants or peptide

Supported prediction tools:

* `syfpeithi`
* `mhcflurry`
* `mhcnuggets-class-1`
* `mhcnuggets-class-2`
* `netmhcpan-4.0`
* `netmhcpan-4.1`
* `netmhc-4.0`
* `netmhciipan-4.1`

- `syfpeithi`
- `mhcflurry`
- `mhcnuggets-class-1`
- `mhcnuggets-class-2`
- `netmhcpan-4.0`
- `netmhcpan-4.1`
- `netmhc-4.0`
- `netmhciipan-4.1`

The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

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