pipeline-guide

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Pipeline Guide

Pipelines allow users to separate steps of a workflow into reusable pieces, automate the start of subsequent steps, specify resources individually, and parallelize workflows by connecting Capsules. The Code Ocean User Interface allows users to connect any number of Data Assets and Capsules in a drag-and-drop interface, while creating a Nextflow script in the background.

A strong understanding of Capsule creation and execution is crucial for constructing complex Pipelines. Refer to the Capsule Guide to learn about Capsule creation. Each Capsule in the Pipeline must have all changes committed and a Reproducible Run performed for it to be used in a Pipeline.

This guide covers the following:

1. The Pipeline UI
2. Components of a Pipeline
3. Managing Pipelines
4. Capsule vs Pipeline Differences
5. How to Run Code in Parallel
6. Nextflow Configurations
7. Pipeline Monitoring
8. Nextflow Artifacts
9. nf-core Pipelines
10. Pipeline Tutorial

Pipeline Overview

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