Custom Pipeline Development

This section walks you through how to build a custom pipeline using an nf-core module, test it on the Biowulf HPC, and adapt it for AWS HealthOmics with Flow-IQ.

We'll follow a real-world example and explain each step, focusing on what needs to happen and why.

Example Scenario

Suppose you’re working with the nf-core Sarek pipeline and then have an idea for an analysis using one step of the pipeline. In particular, you want to build a custom pipeline for your analysis using the Manta germline module.

This guide will show you how to: - Extract and reuse the module - Build a minimal pipeline around it - Test it locally (e.g., on Biowulf HPC) - Prepare and deploy it to AWS HealthOmics using Flow-IQ