Step 2: Understand How nf-core Modules Work

While it might seem like you can just run:

nf-core modules install manta/germline

...it's not quite that simple. nf-core modules are reusable building blocks–not pipelines. You need a proper Nextflow pipeline project to plug the module into. Without this, you'll run into errors because modules can't run on their own. They need a pipeline "framework" to run within else you will get an error like you see below.

So let's move on to the next step and see what we need to do first.