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;
  e96fe2e7-caf5-411f-a12e-bc6d3e6e7076["Output\nstararm_detailed_summary"];
  3 --> e96fe2e7-caf5-411f-a12e-bc6d3e6e7076;
  style e96fe2e7-caf5-411f-a12e-bc6d3e6e7076 stroke:#2c3143,stroke-width:4px;
  4["Bakta"];
  0 -->|output| 4;
  317a9096-601f-4303-961c-c996043b4997["Output\nbakta_annotation_summary"];
  4 --> 317a9096-601f-4303-961c-c996043b4997;
  style 317a9096-601f-4303-961c-c996043b4997 stroke:#2c3143,stroke-width:4px;
  5["Bowtie2"];
  1 -->|output| 5;
  2 -->|output| 5;
  0 -->|output| 5;
  1f7edb9a-d417-4ba2-81ed-6d8fc81b53ca["Output\nbowtie_mapping_stats"];
  5 --> 1f7edb9a-d417-4ba2-81ed-6d8fc81b53ca;
  style 1f7edb9a-d417-4ba2-81ed-6d8fc81b53ca 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;
  9bf68e46-cdcd-4593-9b53-0bcb7d8a9902["Output\njbrowse_output"];
  8 --> 9bf68e46-cdcd-4593-9b53-0bcb7d8a9902;
  style 9bf68e46-cdcd-4593-9b53-0bcb7d8a9902 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