Library Search Workflow

Getting the data to run

cd data
sh ./get_data.sh

To run the workflow to test simply do

make run

We recommend nextflow 24.10 to run.

Installation

You will need to have conda, mamba, and nextflow installed.

Using the Code

This code uses other modules such as the NextflowModules. Make sure to run the following after cloning the code:

git submodule update --init --recursive

Deployment to GNPS2

In order to deploy, we have a set of deployment tools that will enable deployment to the various gnps systems. To run the deployment, use the following commands from the deploy_gnps2 folder.

make deploy-prod

You might need to checkout the module, do this by running

git submodule init
git submodule update