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Overview

Importing New Pipelines

Bioinformaticians can import pipelines from any workflow management system (Nextflow, Custom, WDL) to Quark, and run pipelines with user-configured settings/parameters.

  1. Select Pipelines from the Navigator Menu on the left pane.
  2. Click on the My Pipelines tab.
  3. On the top right, select Import Pipeline and choose a workflow management system. Select Next.
  4. Name your pipeline in Step 1 and follow the prompts on each subsequent page or Steps to configure your pipeline. For example, provide details about the pipeline name, the GitHub repository to be used (Step 2) under Source, and specify the Datasets and Parameters that will be input for your run.
  5. Save the pipeline, and select My Pipeline. You will see it listed, along with the Version details you have provided.
  6. Clone your pipeline to make it ready-to-run on the platform.

For specific pipelines, follow the steps provided for each workflow management system.