Workflows

These workflows are associated with Microbial Variant Calling

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.

Microbial Variant Calling

Last updated Jan 23, 2020

Launch in Tutorial Mode
License: None Specified, defaults to CC-BY-4.0
Tests: ✅ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy Europe Galaxy France Galaxy Main Galaxy Australia Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Dataset\nInput dataset"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nInput dataset"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nInput dataset"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nInput dataset"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nInput dataset"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["snippy"];
  0 -->|output| 5;
  1 -->|output| 5;
  3 -->|output| 5;
  a99eb0be-7b33-44a7-8a7b-3a8f1a93fc82["Output\nsnippy_fasta"];
  5 --> a99eb0be-7b33-44a7-8a7b-3a8f1a93fc82;
  style a99eb0be-7b33-44a7-8a7b-3a8f1a93fc82 stroke:#2c3143,stroke-width:4px;
  a75b877f-f21f-487e-8564-59e2b309cf62["Output\nsnippy_tabular"];
  5 --> a75b877f-f21f-487e-8564-59e2b309cf62;
  style a75b877f-f21f-487e-8564-59e2b309cf62 stroke:#2c3143,stroke-width:4px;
  6["JBrowse"];
  5 -->|snpgff| 6;
  4 -->|output| 6;
  5 -->|snpsbam| 6;
  2 -->|output| 6;
  7eb553ca-d39c-4cae-aa39-c3501c8cada8["Output\njbrowse_html"];
  6 --> 7eb553ca-d39c-4cae-aa39-c3501c8cada8;
  style 7eb553ca-d39c-4cae-aa39-c3501c8cada8 stroke:#2c3143,stroke-width:4px;

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