Learning Outcomes

• Explore Pipelines in Foundry.
• Start creating your own pipelines.
• Understanding the purpose of edges in pipeline development.

Pipeline Guide

Basics

Foundry supports both Via and nf-core pipelines, giving you flexibility in how you design and run analyses.

Via Pipelines

Via pipelines are native Foundry pipelines that you build directly in the UI:

• Created using a drag-and-drop interface with a visual, modular design.
• Reuse modules across multiple pipelines.
• Via pipelines are versioned, making it easy to:
• Track changes over time.
• Re-run analyses with the exact same configuration.
• Maintain reproducibility across projects and collaborators.

Via pipelines are ideal when you want to design workflows visually, collaborate with non-technical users, or incrementally adjust and optimize existing workflows.

nf-core Pipelines

Foundry also supports running nf-core pipelines, which are community-maintained workflows written in Nextflow:

• You can use Public Pipelines listed in pipeline section or import selected nf-core pipelines into Foundry and run them using Foundry’s run environments.
• Pipeline parameters, input datasets, and output locations can be configured through the Foundry interface.
• This allows you to:
• Leverage well-established community pipelines for common tasks.
• Use nf-core workflows while benefiting from Foundry’s sharing, interactive app launching, logging, and resource management features.

To learn how to import and configure nf-core pipelines in Foundry, see the Pipeline Import page.

Reviewing Pipelines

After logging into Via Foundry, go to the Pipelines section using the menu on the left side of the screen. At the top right of the Pipelines page, you’ll see three viewing options:

Category	Description
Released	Pipelines that are publicly available for everyone to use
My Pipeline	Pipelines you’ve created
Shared With Me	Pipelines that others have shared with you or your research

Choose the view that best fits what you’re looking for.

Editing Pipelines

There are two methods to alter pipelines in Via Foundry.

Duplicate a Pipeline

To duplicate an existing pipeline, perform the following steps:

1. Select a pipeline on the pipelines page.
2. Click the kebab menu (three vertical dots) to the right of the Run button.
3. From the expanded menu, select Duplicate Pipeline and confirm by clicking Duplicate.
4. You can now modify the duplicated pipeline as needed.

Forking Pipelines

You can 'Fork' commonly used pipelines. When your pipeline is set to public or edited by other group members, changes to that same revision are not permitted.

Duplicating a pipeline allows you to make modifications without affecting the original pipeline or the work of others. This method provides a convenient way to experiment and improve pipelines while maintaining the integrity of the original version.

Create a New Pipeline

To create a new pipeline, follow these steps:

1. Click the Create a Pipeline button in the upper right.
2. Fill out the required fields in the modal.
3. Click Create.
4. You will be directed to the new pipeline page.
5. Edit the new pipeline as necessary.

Via Foundry includes an autosave feature that automatically saves your pipeline as you work. Additionally, you can use the Save Pipeline button at any time to save manually.

Managing Pipelines

Via Foundry offers additional options for managing pipelines. To delete a pipeline, click the Delete Pipeline button (trash icon).

While creating your pipeline, you can also get the generated Nextflow script by clicking the Download Pipeline button.

Nodes and Edges

Edges serve three main purposes in pipeline development:

1. Establishing Connections: Edges connect the inputs and outputs of multiple processes, allowing data to flow sequentially from one process to another.
2. Defining Input Files or Values: Edges specify input files or values for processes, ensuring that each process receives the required data for execution.
3. Selecting Published Outputs: Edges allow you to identify which outputs should be published in the final output directory. By connecting specific output nodes to the edge, you indicate the files to include in the pipeline's final output.

When creating edges, Via Foundry typically displays available nodes that can be connected, simplifying the connection process between processes.

Node Filtering

Filtering of available nodes for connection is based on factors such as file types for set and file parameters, and names for val parameters. This ensures connections are made between compatible input and output nodes.

This feature of displaying available nodes for connection is also applicable when connecting input parameters to multiple processes, enhancing flexibility in the pipeline creation process.