Workflows

These workflows are associated with Mapping and molecular identification of phenotype-causing mutations

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.

Mapping And Molecular Identification Of Phenotype Causing Mutations

Last updated Oct 18, 2022

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flowchart TD
  0["ℹ️ Input Dataset\nA. thaliana TAIR10 ref genome"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\naligned reads from outcrossed F2 pool"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\naligned reads from Ler mapping strain"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["SnpEff Download"];
  4["Replace parts of text"];
  0 -->|output| 4;
  5["MiModD Variant Calling"];
  4 -->|outfile| 5;
  2 -->|output| 5;
  1 -->|output| 5;
  6["MiModD Extract Variant Sites"];
  5 -->|ofile| 6;
  7["MiModD NacreousMap"];
  6 -->|output_vcf| 7;
  8["MiModD VCF Filter"];
  6 -->|output_vcf| 8;
  9["SnpEff"];
  8 -->|outputfile| 9;
  3 -->|snpeff_db| 9;
  10["MiModD Report Variants"];
  9 -->|snpeff_output| 10;

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 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:

Video: Importing a workflow from URL