Workflows

These workflows are associated with Antibiotic resistance detection

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.

Copy Of GTN Training - Antibiotic Resistance Detection

Last updated Jan 11, 2024

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

Download Galaxy Workflow.ga Galaxy Australia Galaxy France Galaxy Europe Galaxy Main Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Collection\nPlasmids"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["NanoPlot"];
  0 -->|output| 1;
  10["NanoPlot"];
  9 -->|out_fa| 10;
  11["Map with minimap2"];
  0 -->|output| 11;
  9 -->|out_fa| 11;
  12["Racon"];
  9 -->|out_fa| 12;
  11 -->|alignment_output| 12;
  0 -->|output| 12;
  2["Map with minimap2"];
  0 -->|output| 2;
  0 -->|output| 2;
  3["Create assemblies with Unicycler"];
  0 -->|output| 3;
  4["miniasm"];
  2 -->|alignment_output| 4;
  0 -->|output| 4;
  5["Bandage Image"];
  3 -->|assembly_graph| 5;
  6["PlasFlow"];
  3 -->|assembly| 6;
  7["staramr"];
  3 -->|assembly| 7;
  8["Bandage Image"];
  4 -->|gfa| 8;
  9["GFA to FASTA"];
  4 -->|gfa| 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 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: