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 Main Galaxy Australia Galaxy Europe 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;
  ea64464a-e636-4666-b608-1e63e8d1173e["Output\nstararm_detailed_summary"];
  3 --> ea64464a-e636-4666-b608-1e63e8d1173e;
  style ea64464a-e636-4666-b608-1e63e8d1173e stroke:#2c3143,stroke-width:4px;
  4["Bakta"];
  0 -->|output| 4;
  51a03248-4145-40a3-8a21-5063b23c0f48["Output\nbakta_annotation_summary"];
  4 --> 51a03248-4145-40a3-8a21-5063b23c0f48;
  style 51a03248-4145-40a3-8a21-5063b23c0f48 stroke:#2c3143,stroke-width:4px;
  5["Bowtie2"];
  1 -->|output| 5;
  2 -->|output| 5;
  0 -->|output| 5;
  34c13cda-fbe7-4b32-8fd8-8bf9af55f64b["Output\nbowtie_mapping_stats"];
  5 --> 34c13cda-fbe7-4b32-8fd8-8bf9af55f64b;
  style 34c13cda-fbe7-4b32-8fd8-8bf9af55f64b 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;
  d7632e85-75a6-4f19-a277-38ded6081054["Output\njbrowse_output"];
  8 --> d7632e85-75a6-4f19-a277-38ded6081054;
  style d7632e85-75a6-4f19-a277-38ded6081054 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