Pipeline Tutorial
A video walkthrough of all Code Ocean Pipeline features.
Was this helpful?
A video walkthrough of all Code Ocean Pipeline features.
Was this helpful?
This tutorial provides a comprehensive explanation of each Pipeline feature while building an RNA Sequencing pipeline from scratch. The list of shows what features are covered and can be used to skip to the most relevant parts. Each Capsule is available on the Code Ocean Apps Library and all Data Assets have been made public allowing you to follow along and build the Pipeline yourself.
All 3 Data Assets used in the tutorial should be imported to your deployment to ensure they can be used without an IAM role.
Bucket Name:codeocean-public-data
Path:example_datasets/rna-seq-tutorial/GSE157194_reads/
Bucket Name:codeocean-public-data
Path:example_datasets/STAR_GRCh38_GENCODE_Release_21_Index/star_index/
Bucket Name:codeocean-public-data
Path:genomes/hg38_Annotation/
Pipeline overview
Connecting Capsules
Adding Data Assets
main.nf explained
Requirements for using a Capsule in a Pipeline
Considerations when designing a Capsule for a Pipeline
Understanding connection types (parallelization)
Map Paths: source and destination paths
Capsule Settings
Pipeline App Panel
Pipeline settings (cache, IAM roles, error strategies)
Running the Pipeline
Nextflow Artifacts
Debugging strategies
Writing Nextflow and nf-core Pipelines
