Summary

This plugin implements the support for GA4GH APIs for Nextflow.

It currently only supports the Task Execution Service (TES) API.

The Task Execution Schema (TES) project by the GA4GH standardization initiative is an effort to define a standardized schema and API for describing batch execution tasks in a portable manner.

Get Started

To use this plugin, add it to your nextflow.config:

plugins {
  id 'nf-ga4gh'
}

Configure the TES executor:

process.executor = 'tes'

[!NOTE]

While the TES API is designed to abstract workflow managers from direct storage access, Nextflow still needs to access the shared work directory used by your TES endpoint.

For example, if your TES endpoint is located in Azure and uses Azure Blob storage to store the work directory, you still need to provide the necessary Azure credentials for Nextflow to access the Blob storage.

Examples

Endpoint

[!TIP]

It is important that the endpoint is specified without the trailing slash; otherwise, the resulting URLs will not be normalized and the requests to TES will fail.

The default endpoint is http://localhost:8000

tes {
    endpoint = '<endpoint>'
}

Authentication

The TES API supports multiple forms of authentication:

Basic

tes {
    basicUsername = '<username>'
    basicPassword = '<password>'
}

API key

tes {
    apiKeyParamMode = '<mode>' // 'query' or 'header'
    apiKeyParamName = '<param-name>'
    apiKey = '<key>'
}

OAuth

tes {
    oauthToken = '<token>'
}

TES Server

You can deploy a local Funnel server using the following commands:

curl -fsSL https://ohsu-comp-bio.github.io/funnel/install.sh | bash

funnel server run

License

Apache License 2.0