Funnel

OHSU Comp Bio

⚠️ Nextflow support is currently in development and requires a few additional steps to run which are included below.

Nextflow

Nextflow is a workflow engine with a rich ecosystem of pipelines centered around biological analysis.

Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.

Its fluent DSL simplifies the implementation and the deployment of complex parallel and reactive workflows on clouds and clusters.

Since Nextflow includes support for the TES API, it can be used in conjunction with Funnel to run tasks or to interact with a common TES endpoint.

Getting Started

To set up Nextflow to use Funnel as the TES executor, run the following steps:

1. Install Nextflow

git clone https://github.com/nextflow-io/nextflow -b tes-update-1.1

cd nextflow

make compile

This will create a new launch.sh file that can be used to run the Nextflow workflow below.

2. Update Nextflow Config

Add the following to your nextflow.config in order to use the GA4GH TES plugin:

plugins {
  id 'nf-ga4gh'
}

process.executor = 'tes'
tes.endpoint = 'http://localhost:8000'   # <--- Funnel's default address

3. Start Funnel and Run Workflow

Finally, start the Funnel server and launch Nextflow:

funnel server run

alias nextflow=~/nextflow/launch.sh  # <--- Change this line to match your local nextflow directory

nextflow run main.nf -c nextflow.config

Additional Resources