Learning Outcomes

• How to access and select pipelines.
• How to launch pipelines.
• How to configure pipelines.

Run a Pipelines

Using the RNA-Seq Pipeline as an example, lets run a pipeline in Via Foundry, follow the steps below.

Explore and select a pipeline

1. Access Pipelines: Select the Pipelines tab. From there, you can explore publicly available pipelines. Select the pipeline of interest by clicking on the tile.
2. Explore Pipelines: Explore publicly released pipeline, Pipelines you've created, and Pipelines shared with you.
3. Select RNA-Seq Pipeline: Search for RNA-Seq and select the RNA-Seq Pipeline tile.
4. Select a Pipeline: After loading the selected pipeline, locate and click the Run button at the top right corner of the page.

Configure a Run

1. Select/Create a Project: Runs live in projects. Here, you can create a new project by typing the name of the new project and selecting Create "<your project name>".

2. Input Run Name: Once you have created or selected your project, enter a run name. Then click Create to navigate to the "Run Page" for you new run.

Set Run parameters

On the "Run Page," you will initially see an orange Waiting button in the header. Hover over the "Waiting" status to see what you need to configure.

1. Configure Run Settings:

   • Run Environment: Select the environment you wish to use, as detailed in the Profile documentation.
   • Work Directory: If you are submitting your jobs to an HPC/cluster environment, specify the full path to the work directory where workflows will execute. Otherwise, this value will be auto-filled.

2. Set Run Inputs:

   Enter the required values and files that define:

   • The dataset to be processed, and
   • The processing parameters relevant to your workflow.

3. Start the Run: Upon fulfilling all required settings, the Waiting button will change to a green Run button. Click this button to start the run. For a comprehensive understanding of each module on the run page, please review the Run Guide.