Import nf-core pipelines

A general introduction to importing nf-core.

Import an nf-core pipeline

  1. From the Sidebar, create a new Pipeline by Import from nf-core

  2. Select the pipeline name and version

  3. Click on Import.

Successful Import

Attaching Data and Setting Parameters

Input data will be required for nf-core pipelines. Data Assets of any type can be attached to nf-core pipelines.

  • Read the file in the /pipeline folder to understand the required input files and parameters.

    • The "Usage" section of the Readme will have links to more detailed usage documentation and parameter documentation.

  • The Pipelines parameters are generally located in the nextflow.config file. These can be manually changed here or via the Pipeline's automatically generated App Panel.

To use External Data Assets in a pipeline, Assumable Roles must be configured. If this isn't configured in your deployment or you're unsure if it is, contact your Code Ocean admin.

Running the Pipeline

The nf-core Pipeline can be run like any other Pipeline in Code Ocean, by pressing Reproducible Run.

Exception Handling

If the Pipeline has failed, we recommend you set the following in the Pipeline Settings:

  • Run using On Demand Instances is recommended. Spot resources may drop out, requiring Retry set to Max Attempts and pressing Reproducible Run if you repeatedly lose machines due to availability.

  • Run with Cache from the Previous Run to avoid rerunning the part of the pipeline that completed successfully.

  • Set the Error Strategy to Retry with Number of Retries to 10. This will try to resolve internal conflicts due to endpoints and/or service interruptions before stopping.