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Workflow: Variant Calling

Create a Galaxy workflow

Galaxy provides the option to extract a workflow based on the steps you just followed and the tools and parameters used.

New to Galaxy? First try the introduction and then learn some key tasks

Variant calling

  • Log in to your Galaxy instance (for example, Galaxy Australia,

Before we create a workflow for variant calling, we need the correct files in our current Galaxy history. We can get these files in two ways:

  • Either follow the tutorial on variant calling

  • Or, obtain the files from a Shared History (Galaxy Australia only).

    • Go to Shared Data
    • Click Histories
    • Click Variant_calling_with_snippy
    • Click Import (at the top right corner)
    • The analysis should now be showing as your current history.

When you have completed this tutorial or imported the history, you will have the correct files in your history panel.

Extract the Workflow

  • In the history panel, click on the cog icon.
  • Click Extract Workflow
  • If all looks ok, click Create Workflow
  • In the centre panel, click edit

This brings up the workflow canvas, a space for graphically viewing and re-arranging your workflow.


  • Drag the panes around until your workflow is clear.
  • In the top right corner click on the cog icon and Save
  • Click on the cog icon again and Run

    • Send results to a new history: Yes
    • Check all input files are correct and change if necessary
    • In the top right corner Run workflow
  • This workflow will now run.

  • In the History panel, click on the View all histories icon view hist
  • Find your workflow history and Switch to it.

To see all your workflows, go to the top panel in Galaxy and click Workflow.

  • You can edit or run workflows from here by clicking on the drop-down arrow next to each workflow.

What’s next?

To use the tutorials on this website:

  • ← see the list in the left hand panel
  • ↖ or, click the menu button (three horizontal bars) in the top left of the page

You can find more tutorials at the Galaxy Training Network: