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Pipeline Guide

Output Parameters

The Output Parameters section is located just below the Input Parameters section in the left sidebar. To add an output parameter to your canvas, simply drag and drop it from the Output Parameters section.

Output/Input sidebar

Each Output Parameter is represented by a green circle.
The name of this circle corresponds to the published directory name where the associated output files will be transferred.

You can rename an output parameter by clicking the pencil icon next to the circle. This allows you to customize the directory name for the output files.

Output parameter circle

By defining and configuring output parameters, you control which files are published and how they are organized into directories within your pipeline.

Output parameter settings

Tips:

  • If you do not want to publish certain output files, leave their output nodes unconnected. Only files linked to defined output parameters will be transferred to the published directory.
  • If you want to transfer multiple outputs into the same directory, you can reuse the same name for different output parameters. When the pipeline runs, files from different output nodes that share the same output parameter name will be published into the same directory.

Publish to Web Directory

In the output parameter configuration modal, there is a Publish to Web Directory option.
When enabled, this option transfers the selected published files to the Run page → Report tab.

This allows users to easily access and interact with summary reports (e.g., html,tsv,csv,h5ad,png and other image formats)

These published files can then be viewed directly or explored with compatible applications, for example:

  • Shiny apps for differential expression analysis (e.g., DEBrowser)
  • Interactive single-cell viewers (e.g., cellxgene)

By using Publish to Web Directory, you make key results and visualizations easily accessible from within Foundry.

Report Ordering

You can control the ordering of run reports in Foundry by adding the @report_order flag to your nextflow.config file.

  • The line must start with //* (a special comment recognized by Foundry).
  • The value is a list of folder names or glob patterns.
  • You only need to list the folders you want to appear at the top. All other folders will follow in their default order.

Example

Add a line like this to your nextflow.config:

//* @report_order: ['folder1', 'folder2', 'folder3_*']
In this example:
  • folder1 will appear first in the report list.
  • folder2 will appear second.
  • Any folder matching folder3_* (e.g., folder3_qc, folder3_stats) will appear next.
  • All other folders will be listed after these, in their default order.