.codeocean

Pipelines created in Code Ocean v2.22 and beyond will have a /.codeocean folder, which will materialize all Pipeline files and settings in a git repo. These files are read only, and will be automatically edited when needed. The user will never need to edit these files directly.

app-panel.json

This file records the Pipeline's App Panel. For Pipelines created from the UI, this file will record from which Capsules in the Pipelines App Panels have been imported. For nf-core Pipelines or manually written main.nf files, app-panel.json will record all of the parameters. With this file, updates to the App Panel can be committed to git.

datasets.json

This file records which Data Assets are attached to the Pipeline. With this file, the Data Assets attached to the Pipeline can be committed to git.

nextflow.json

This file records each Capsule used in the Pipeline, including the version, whether is has an App Panel, the resources it was given to run, and the IDs of its inputs and outputs. nextflow.json is only present when the Pipeline Editor is used and the main.nf file has not been unlocked. When the main.nf file is unlocked, this file is deleted. With this file, the logical representation of the Pipeline can be committed to git.

pipeline-layout.json

This file records the layout of the Capsules and connections in the Pipeline Editor and is only present when the Pipeline Editor is used and the main.nf file has not been unlocked. When the main.nf file is unlocked, this file is deleted. With this file, the visual representation of the Pipeline can be committed to git.

settings.json

This file records the Pipeline Settings, such as the Nextflow version, instance type, running with cache, the AWS IAM Role, error strategy, and debugging options. With this file, settings applied across the Pipeline can be committed to git.