NP³ MS Workflow Nextflow

To run the workflow to test simply do

make run

The NP3 testing dataset is used by default.

To learn more about the NP3 pipeline, please checkout the repository.

To update the NP³ code with the latest commit and setup do

make update_np3

To learn NextFlow checkout this documentation:

https://www.nextflow.io/docs/latest/index.html

Installation NP³ MS Workflow with Nextflow

You will need to have conda and mamba installed to run things locally.

First initialize the submodules, run:

make init_modules 

Create the np3_nextflow conda environment stored in: bin/environment_np3_nextflow_unix.yml

mamba env create -f bin/environment_np3_nextflow_unix.yml 

Then, install further nodejs dependencies and execute the NP³ setup automatically by running:

sh bin/install_setup.sh

You are good to go!

Or, the last installation step can be executed manually with the following steps:

Activate the np3_nextflow environment:

mamba activate np3_nextflow 

Then, install some additional nodejs packages and audit the installation:

npm install shelljs@0.8.4 commander@5.1.0

Finally, go to the 'bin/NP3_MS_Workflow' directory and run the NP³ MS Workflow setup (check installed packages, compile some code, aggregate some data from UNPD-ISDB and download large data from spec2vec):

cd bin/NP3_MS_Workflow
node np3_workflow.js setup 

You are good to go!

Deployment to GNPS2

Check Nexftlow template instructions from Mingxun Wang.