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 question
License: MIT
Tests: ✅ Results: Not yet automated

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;
  0085b77d-6d65-4e39-be1e-317470ac60ec["Output\nstararm_detailed_summary"];
  3 --> 0085b77d-6d65-4e39-be1e-317470ac60ec;
  style 0085b77d-6d65-4e39-be1e-317470ac60ec stroke:#2c3143,stroke-width:4px;
  4["Bakta"];
  0 -->|output| 4;
  3e7f1c16-97be-4e89-a909-a928c14e7182["Output\nbakta_annotation_summary"];
  4 --> 3e7f1c16-97be-4e89-a909-a928c14e7182;
  style 3e7f1c16-97be-4e89-a909-a928c14e7182 stroke:#2c3143,stroke-width:4px;
  5["Bowtie2"];
  1 -->|output| 5;
  2 -->|output| 5;
  0 -->|output| 5;
  3b8ab1bd-5f5e-4d32-ba9e-6f08820f43b3["Output\nbowtie_mapping_stats"];
  5 --> 3b8ab1bd-5f5e-4d32-ba9e-6f08820f43b3;
  style 3b8ab1bd-5f5e-4d32-ba9e-6f08820f43b3 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;
  280d8680-8066-4987-a781-53ab0eb7c3d7["Output\njbrowse_output"];
  8 --> 280d8680-8066-4987-a781-53ab0eb7c3d7;
  style 280d8680-8066-4987-a781-53ab0eb7c3d7 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 galaxy-upload 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: