Nextflow

Nextflow provides a modern execution stack for bioinformatics, featuring a Groovy-based DSL with reactive streams. It supports multiple backends including Docker and runs on any POSIX-compatible system, with Windows support through WSL.

Prerequisites

• Java 8 or higher

• Docker

• Optional: cURL, git, Conda

• For Windows only: WSL

Getting Started

The following software and workflow are required and will be downloaded, installed, and used as part of this tutorial:

• Nextflow

• 02_download_collection_files.nf

• nextflow.config

Getting the Example Workflow

Clone with Git

git clone https://github.com/DNAstack/dnastack-client-library-worked-examples.git

Or Download and Unzip

It is assumed that all commands will be run from the root directory of this repository on your local machine. From the directory where you’ve downloaded the examples repository.

cd dnastack-client-library-worked-examples/

Installing Nextflow

Download and install Nextflow by one of the following methods.

Using cURL or direct from this link, and allow execution permission

curl -o nextflow -L https://get.nextflow.io # Or directly from web link

chmod +x nextflow

Or Using Conda

conda install -c bioconda nextflow

Running the workflow

To run the workflow

./nextflow run --config examples/nextflow/nextflow.config examples/nextflow/02_download_collection_files.nf

Output files can be found in the current directory.

Nextflow Tower

Nextflow Tower provides centralized monitoring and logging for your workflows. To enable Tower:

1. Add the following to the configuration file nextflow.config. Replace with your specific access token.

docker.enabled = true
tower {
    enabled = true
    accessToken = '<YOUR TOKEN>'
}

1. Find your access token in the user menu under "Your tokens"

2. View workflow details in the "runs" section