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Quick Start: Running Pipelines

This guide walks you through taking your first steps — whether you are a bench scientist running your first pipeline, or a bioinformatician importing a new pipeline.

Running Pipelines on Quark

Bench scientists and bioinformaticians can run pipelines on Quark in two ways:

  • Quark enables users (e.g. bench scientists) to run nf-core and AWS Healthomics pipelines out-of-the-box from the Launchpad.
  • Users (e.g. bioinformaticians) can also import a pipeline from different workflow management systems (Nextflow, WDL, Snakemake) and configure them according to their project needs from My Pipelines.

Getting Started: Bench Scientists

If you are a bench scientist looking to run a pipeline for the first time:

  1. Log in to Quark using your credentials
  2. From the Navigator pane, select Pipelines
  3. Click on the Launchpad tab
  4. Use the search bar or category filters to find a pipeline suited to your experiment (e.g. RNA-Seq, DNA-Seq, Protein Folding)
  5. Click on a pipeline to view its description, requirements, version, and tags
  6. Click Run and follow the step-by-step guided configuration:
  7. Provide a Run Name
  8. Configure Input Parameters (e.g. input files, sequences, protocol settings)
  9. Click Review to validate your inputs
  10. Click Next to submit your run
  11. Monitor the status of your run from the Runs tab

Tip: If any required inputs are missing, an error will be shown on the Review screen. Check all parameters before submitting.

Next Steps: Navigate to Ready to Run Pipelines for a detailed guide on how to configure and launch a pipeline.

Getting Started: Bioinformaticians

If you are a bioinformatician who needs to import or build your own pipeline:

  1. Log in to Quark
  2. From the Navigator pane, select Pipelines
  3. Click on the My Pipelines tab
  4. Click Import Pipeline and follow the import flow for your workflow format:
  5. Once your pipeline is ready, version and publish it so it becomes available to run on the platform
  6. Submit and track runs via the Runs tab