Bioinformatics Nextflow Research

This repository hosts some Nextflow workflow tutorials:

1. BRH Demo Notebooks

A collection of tutorial notebooks that are run on a local execution of Nextflow in the BRH Nextflow Workspace.

2. MIDRC Demo Notebooks

A collection of tutorial notebooks that are specific to MIDRC use cases. These notebooks demonstrate Nextflow workflows run on a conda virtual environment and containerized batched workflows run on the cloud using CPU and GPU resources.

View Static Notebooks

Some of the notebooks can be viewed without having to execute the code by opening the html versions in a browser. These are located in the folder nextflow_notebooks/static_notebooks. Some of the notebooks can also be viewed on the BRH Example Analysis Page (https://brh.data-commons.org/resource-browser).

Run Notebooks on the Biomedical Research Hub

To run the interactive notebooks in the Biomedical Research Hub (BRH), go to https://brh.data-commons.org/workspace, login, select a BRH Workspace Account, and launch a Nextflow workspace computational environment that is provisioned with either CPU or GPU resources. Once a workspace is open, upload the desired notebook to workspace image and run the notebook. Note that some of the MIDRC batch workflows require the user to first build and push a containerized Nextflow image to the BRH Nextflow AWS Elastic Container Repository and to configure the AWS account resources and containers in the notebook.