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 France Galaxy Main Galaxy Australia Galaxy Europe 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;
  13e72162-3f36-44ab-a8d1-c52976b43d27["Output\nstararm_detailed_summary"];
  3 --> 13e72162-3f36-44ab-a8d1-c52976b43d27;
  style 13e72162-3f36-44ab-a8d1-c52976b43d27 stroke:#2c3143,stroke-width:4px;
  4["Bakta"];
  0 -->|output| 4;
  e722f8c7-5ba8-49c8-bdee-56b106fa7fbc["Output\nbakta_annotation_summary"];
  4 --> e722f8c7-5ba8-49c8-bdee-56b106fa7fbc;
  style e722f8c7-5ba8-49c8-bdee-56b106fa7fbc stroke:#2c3143,stroke-width:4px;
  5["Bowtie2"];
  1 -->|output| 5;
  2 -->|output| 5;
  0 -->|output| 5;
  a9f79824-ff35-475b-8659-03425b7af733["Output\nbowtie_mapping_stats"];
  5 --> a9f79824-ff35-475b-8659-03425b7af733;
  style a9f79824-ff35-475b-8659-03425b7af733 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;
  3d9b31d2-75f5-4874-b444-0ff973aebf14["Output\njbrowse_output"];
  8 --> 3d9b31d2-75f5-4874-b444-0ff973aebf14;
  style 3d9b31d2-75f5-4874-b444-0ff973aebf14 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: