What is Nextflow?

Nextflow is a workflow management system used by bioinformaticians to execute complex pipelines. Inside the SURF Research Cloud, Nextflow (v.23.10.0) is available through EESSI (pronounced "easy"). 

Working with Nextflow inside the SRC

Once a workspace has been created, access it and create a conda environment inside. If this is your first time using conda, please check the miniconda tutorial or the in-depth instructions on how to install it.

Inside the workspace, follow these steps:

Example: 

conda create -n Nextflow

Enter the environment:

conda activate Nextflow

If this is your first time working with Nextflow, follow the official tutorial provided by Nextflow. 

Inside the terminal, clone the training repository from Nextflow:

git clone https://github.com/nextflow-io/training.git

Important notice: You might need to install tools. The best practice is to install these tools via conda. Sometimes, you might need to add channels yourself. Please check the workflow steps and ensure all tools are installed before running the pipeline.