jawadqur / nextflow-wrapper

WARNING

This is a very basic proof of concept repository for running Nextflow workflows remotely via Golang api. Use with caution!

Overview

This repository contains Golang code to execute Nextflow workflows through a basic api as subprocesses. The goal is to demonstrate a simple way to invoke Nextflow workflows from Go code.

The main logic is in main.go which does the following:

• Construct a command to invoke a Nextflow workflow
• Execute the command as a subprocess
• Stream stdout and stderr to log and to the http response.

There is also a simple API defined:

• /exec - Execute the hello workflow
• /exec/{workflow} - Execute a specific workflow by name

Overall this shows a straightforward pattern for running Nextflow remotely from Golang, but lacks robustness for production use. Treat as a simple proof of concept only!

Dev/ test

Either using the Dockerfile or just download nextflow binary and have JDK on your workstation.

Update the nextflow binary location in code.

If you have nodemon installed you can have a hot reloading dev environment set up like:

Dependencies

go mod download

Run dev

nodemon --exec go run main.go --signal SIGTERM