Code Ocean User Guide
v3.6.0
v3.6.0
  • Welcome to Code Ocean
  • Onboarding
    • Quick Start Guides
      • Create a Capsule in 5 minutes
      • Create a Pipeline in 5 minutes
    • Video Library
  • Key Concepts
  • Capsule Guide
    • The Capsule Interface
      • File Navigation/App Builder Panel
      • Editor Panel
      • Reproducibility Panel
    • The Structure of a Capsule
      • Metadata
      • Environment
      • Code
      • Data
      • .codeocean
      • Scratch
      • Results
    • Reproducible Runs
    • Version Control
      • Importing a Capsule from a Git Provider
      • Clone via Git...
    • Managing Capsules
      • Sharing a Capsule with Secrets
      • Exporting Capsules to your Local Machine
    • Secret Management Guide
      • Setting a Secret in the Account Settings Page
      • Accessing a Secret in a Capsule
  • Setting up the Environment
    • Selecting a Starter Environment
    • Package Managers and Adding Packages
    • Installing R packages
    • Environment Variables
    • Build Log
    • Post-Install Script
    • Compute Resources
  • Working in a Cloud Workstation
    • Launching a Cloud Workstation
      • Running RShiny in Code Ocean
      • Running Streamlit in Code Ocean
      • Using Terminal in Code Ocean
      • Using Ubuntu Desktop in Code Ocean
      • Using MATLAB in Code Ocean
      • Using VS Code in Code Ocean
    • Exiting a Cloud Workstation Session
  • Data Assets Guide
    • Types of Data Assets
    • Creating a New Data Asset
    • Capturing a Result
      • Provenance of the Result Data Asset
    • Using Data Assets in a Capsule
    • Managing Data Assets
      • Finding Data Assets
        • Custom Metadata
  • Pipeline Guide
    • The Pipeline UI
      • File Tree System
      • Pipeline App Panel
      • Timeline
    • Components of a Pipeline
      • Nextflow File
      • Capsules
      • Data
      • Results Bucket
      • Map Paths
      • Capsule Settings
      • Pipeline Settings
      • .codeocean
    • Managing Pipelines
      • Exporting Pipelines to your Local Machine
    • Capsule vs Pipeline Differences
    • How to Run Code in Parallel
    • Nextflow Configurations
    • Pipeline Monitoring
      • Monitoring Dashboard
      • Task Details
    • Nextflow Artifacts
    • nf-core Pipelines
      • Import nf-core pipelines
      • nf-core RNASeq Tutorial
        • iGenomes
    • Pipeline Tutorial
  • Release Capsules and Pipelines
    • Creating and Using Release Capsules
    • Creating Release Pipelines
    • Internal Releases
  • Collections
  • Code Ocean Apps
    • Genomics
    • Cheminformatics
    • Visualization
    • Machine Learning
    • Data Connectors
    • Quality Control
    • Use Cases and Examples
      • CombFold Pipeline
      • Data Connector Example
      • Gene Set Enrichment Overview
      • RNASeq Quantification Pipeline
  • App Panel Guide
    • App Builder User Interface
      • Validation pattern for strings
    • Passing App Panel's Parameters to the Script
    • Releasing an App Panel Capsule
    • Executing an App Panel Capsule
  • MLflow Guide
    • Enable MLflow Tracking
    • MLflow UI
    • Creating Models
    • MLflow Permissions
  • Models Guide
    • Creating Models
    • Managing Models
  • Git Provider Integration Guide
    • Setting up the Integration
    • Using Git Provider Integration
  • Code Ocean API
    • Authentication
    • Errors
    • Capsule
    • Computation
    • Data Asset
    • Python SDK
  • More Support
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  • Version
  • Compute Resources
  • Arguments

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  1. Pipeline Guide
  2. Components of a Pipeline

Capsule Settings

This section will explain how to configure the settings of the Capsule in a Pipeline, including the Capsule version, resources, and command line arguments.

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To open the Capsule Settings, double click on a Capsule or hover over a Capsule and click the gear icon. It will open the this box:

At the top of the Capsule Settings is the name of the Capsule with an information icon to view the description of the Capsule from the Capsule metadata. Open the Capsule by clicking Go to this capsule.

Version

If the Capsule has been released or it is from the Code Ocean Apps Library, there is a dropdown menu to select the version of the Capsule to use in the Pipeline, and a button to Use the Latest Version. The version used by the Pipeline will remain unchanged if a new version of the Capsule is released.

Compute Resources

Once a Capsule is added to a Pipeline, it will inherit the resources selected in the Capsule's environment editor. The Capsule Settings menu can then be used to modify the resources allocated to the Capsule, independent of those set in the environment editor.

Each CPU based Capsule can be allocated a maximum of 192 cores and 4096 GB RAM. GPU based Capsules can be allocated a maximum of 8 GPUs, 192 cores and 4096 GB RAM.

By default all Capsules will run on dedicated machines. Pipelines can be configured to run on spot instances in the Pipeline Settings.

When a power-of-two value (e.g. 8, 16, 32 GB) is requested for Capsule memory, Code Ocean automatically adjusts the value in main.nf to 15/16 of the requested amount. This helps optimize resource allocation and avoid unintended higher costs.

Arguments

Capsule run script arguments can be entered into the Capsule Settings box for each Capsule. Arguments must be separated by spaces. If an argument includes a space, such as the title of a plot, it should be in quotes.

It is recommended to create an App Panel for the Pipeline rather than supplying arguments. If there is an App Panel for the Pipeline, the Arguments section will be disabled.