Create a pipeline in 5 minutes

Before creating the pipeline, convert all local data files into Data Assets as the same data will be used in the pipeline. Using data assets will improve the performance of the pipeline by ensuring data is passed smoothly through Nextflow channels. To learn more about data assets refer to the Data Assets Guide.

Create a data asset from sample-data.txt with the following steps:

1. Download the sample-data.txt file to your computer

2. Click Manage Datasets at the data folder in your file tree system

3. Click Attach Data

4. Click Add Dataset

5. Select Local files

6. Click Next

7. Click Choose Files

8. Select sample-data.txt file

9. Name the dataset and default folder Sample_Data and a tag of test.

10. Click Add dataset

Create a new Pipeline

To navigate to the Pipeline:

1. Click Pipeline

   
2. Click Add Pipeline, Create New

   

A new Pipeline can be created by cloning from your organization's private Git account. This enables the use of Code Ocean's Git Sync feature which ensures your Code Ocean Pipeline and the associated Git repository stay in sync.

Add the Capsule to the Pipeline

In the Add Capsules menu, find "My First Capsule" and drag it onto the pipeline building area.

Add a Code Ocean Apps Capsule

Pre-built capsules can be leveraged from the Code Ocean Apps Library in Pipelines by dragging and dropping them into the Pipeline Builder UI.

Form a Capsule Connection

To ensure that the capsule's results are saved after each run, connect the capsule to the results bucket:

1. Click + at the bottom of the capsule

2. To form a Capsule Connection, drag the + to the results bucket

Attach the Data Asset

To attach the Sample_Data data asset to the pipeline's data folder:

1. Click Manage Datasets at the data folder of the file tree system

2. Click Attach Data

3. Select the Sample_Data data asset from the dropdown menu

   
4. Click and drag the Sample_Data data asset from the data folder to the pipeline building area

   
5. Create a Capsule Connection from the Sample_Data dataset to the capsule.

Passing the file to the Destination Capsule

In the current configuration of the pipeline, the capsule expects to find a sample-data.txt file in the data folder but finds a folder named Sample_Data. To correct this:

1. Click on the gear in the middle of the data to capsule connection

2. In the pop-up menu set the source path to data/Sample_data/sample-data.txt

3. To run the pipeline click Reproducible Run at the top right of the pipeline page

4. Once the run is complete, the contents of the result bucket can be viewed in the Timeline

This tutorial demonstrated how to create a simple single-capsule pipeline but the Visual Pipeline Builder also supports the creation of complex multi-capsule pipelines.

Viewing the Pipeline

There are four options for viewing the pipeline:

• Zoom in - magnifies the pipeline

• Zoom out - minimizes the pipeline

• Fit view - shows the pipeline in its entirety

• Eye toggle - shows the:

  • Connection types

  • CPUs

  • Memory

  • Data Type: Internal, External and Result

  • Capsule Type: Release, Code Ocean Apps

Export A Pipeline

Pipelines can be exported from the Pipeline menu.

Exporting the pipeline automatically creates nextflow.config and REPRODUCING.md files which contain all the configurations and instructions required to run the pipeline on a local machine.

Export a Pipeline