These workflows are associated with Calling variants in diploid systems

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.


Last updated Jan 22, 2020

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Tests: ❌ Results: Not yet automated

flowchart TD
  0["ℹ️ Input Dataset\nGIAB-Ashkenazim-Trio-hg19.bam"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["SnpEff Download"];
  2["ℹ️ Input Dataset\nGIAB-Ashkenazim-Trio.tabular"];
  style 2 stroke:#2c3143,stroke-width:4px;
  0 -->|output| 3;
  3 -->|output_vcf| 4;
  5["SnpEff eff:"];
  4 -->|out_file1| 5;
  1 -->|snpeff_db| 5;
  6["GEMINI load"];
  5 -->|snpeff_output| 6;
  2 -->|output| 6;
  6 -->|outfile| 7;
  6 -->|outfile| 8;
  6 -->|outfile| 9;

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands-on: Importing a workflow
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on galaxy-upload Import at the top-right of the screen
  • Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  • Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure: