Workflow Developer Guide

This guide is for people writing Nextflow pipelines that run on the platform's EKS cluster. It covers how to integrate your workflow with Tracker, what cluster features are available to your pipeline, and how to use AI-powered tools for investigating and optimizing runs.

What's Covered

1. tracker.yml Reports -- How to configure which output files appear as reports in Tracker's Reports tab.
2. Cluster Features -- Resource directives, scheduling hints, S3 staging, error handling, and bin-packing considerations provided by the nf-k8s-cloud executor.
3. Claude Skills -- AI-powered tools for investigating failures, optimizing resource allocations, and debugging Nextflow configuration.

Prerequisites

• Runs are submitted via the tracker CLI and execute on EKS with the nf-k8s-cloud executor.
• The nf-tracker plugin sends lifecycle events to Tracker automatically -- no workflow-side configuration is needed for basic run tracking.
• Tracker displays run status, task details, cost analysis, and outputs without any changes to your pipeline code. The developer guide covers optional integrations (reports) and cluster-specific features you can take advantage of.