Pipeline Tutorial
A video walkthrough of all Code Ocean Pipeline features.
This tutorial provides a comprehensive explanation of each Pipeline feature while building an RNA Sequencing pipeline from scratch. The list of chapters 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.
Chapters
00:00 Pipeline overview
02:24 Connecting Capsules
06:01 Adding Data Assets
06:25 main.nf explained
07:42 Requirements for using a Capsule in a Pipeline
08:28 Considerations when designing a Capsule for a Pipeline
14:17 Understanding connection types (parallelization)
29:20 Map Paths: source and destination paths
33:10 Capsule Settings
34:53 Pipeline App Panel
37:30 Pipeline settings (cache, IAM roles, error strategies)
44:35 Running the Pipeline
47:30 Nextflow Artifacts
50:24 Debugging strategies
53:00 Writing Nextflow and nf-core Pipelines
Data Assets
All 3 Data Assets used in the tutorial should be imported to your deployment to ensure they can be used without an IAM role.
Paired End Reads (8GB)
Bucket Name: codeocean-public-data
Path: example_datasets/rna-seq-tutorial/GSE157194_reads/
STAR Index (28GB)
Bucket Name: codeocean-public-data
Path: example_datasets/STAR_GRCh38_GENCODE_Release_21_Index/star_index/
Annotation File (1GB)
Bucket Name: codeocean-public-data
Path: genomes/hg38_Annotation/
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