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'

Configuration

plugins {
    id 'nf-ga4gh'
}

process {
    executor = 'tes'
    container = 'quay.io/nextflow/bash'
}

tes {
    endpoint = 'http://localhost:8000'
    timeout = 30
    pollInterval = '10s'
    tags {
        tag1 = 'abc'
        tag2 = 'xyz'
    }
}

Endpoint

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>'
}

Examples

Deploy a local 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