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;
  9ad61736-6276-4fb7-b78d-d3dfdf8816f8["Output\nstararm_detailed_summary"];
  3 --> 9ad61736-6276-4fb7-b78d-d3dfdf8816f8;
  style 9ad61736-6276-4fb7-b78d-d3dfdf8816f8 stroke:#2c3143,stroke-width:4px;
  4["Bakta"];
  0 -->|output| 4;
  258079c2-912e-4cd0-946e-874b0bd3d35f["Output\nbakta_annotation_summary"];
  4 --> 258079c2-912e-4cd0-946e-874b0bd3d35f;
  style 258079c2-912e-4cd0-946e-874b0bd3d35f stroke:#2c3143,stroke-width:4px;
  5["Bowtie2"];
  1 -->|output| 5;
  2 -->|output| 5;
  0 -->|output| 5;
  1f98083c-0137-4735-a754-9f6d36676273["Output\nbowtie_mapping_stats"];
  5 --> 1f98083c-0137-4735-a754-9f6d36676273;
  style 1f98083c-0137-4735-a754-9f6d36676273 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;
  30238ee4-f711-4be9-b511-ef268bbce3ce["Output\njbrowse_output"];
  8 --> 30238ee4-f711-4be9-b511-ef268bbce3ce;
  style 30238ee4-f711-4be9-b511-ef268bbce3ce 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:

Video: Importing a workflow from URL