Workflows

These workflows are associated with Identification of AMR genes in an assembled bacterial genome

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.

mrsa AMR gene detection
Bazante Sanders, Bérénice Batut

Last updated Jan 23, 2024

Launch in Tutorial Mode
License: MIT
Tests: ✅ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy Australia Galaxy Europe Galaxy Main Galaxy France Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Dataset\ncontigs"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nforward_reads"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nreverse_reads"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["staramr"];
  0 -->|output| 3;
  d890654f-2148-41b0-99bf-b1ab847374a0["Output\nstararm_detailed_summary"];
  3 --> d890654f-2148-41b0-99bf-b1ab847374a0;
  style d890654f-2148-41b0-99bf-b1ab847374a0 stroke:#2c3143,stroke-width:4px;
  4["Bakta"];
  0 -->|output| 4;
  5d1fcb5f-6022-426d-a552-188e2883707a["Output\nbakta_annotation_summary"];
  4 --> 5d1fcb5f-6022-426d-a552-188e2883707a;
  style 5d1fcb5f-6022-426d-a552-188e2883707a stroke:#2c3143,stroke-width:4px;
  5["Bowtie2"];
  1 -->|output| 5;
  2 -->|output| 5;
  0 -->|output| 5;
  bee614c2-aa4a-4700-b339-c8a1869bb0fe["Output\nbowtie_mapping_stats"];
  5 --> bee614c2-aa4a-4700-b339-c8a1869bb0fe;
  style bee614c2-aa4a-4700-b339-c8a1869bb0fe stroke:#2c3143,stroke-width:4px;
  6["Select"];
  3 -->|detailed_summary| 6;
  7["Table to GFF3"];
  6 -->|out_file1| 7;
  8["JBrowse"];
  4 -->|annotation_gff3| 8;
  7 -->|output| 8;
  5 -->|output| 8;
  34f69a98-08c7-476f-bac4-a7cd6d9dfd1a["Output\njbrowse_output"];
  8 --> 34f69a98-08c7-476f-bac4-a7cd6d9dfd1a;
  style 34f69a98-08c7-476f-bac4-a7cd6d9dfd1a 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: