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;
  d2e300e1-7789-4dab-ae9b-62f7bf8131c9["Output\nstararm_detailed_summary"];
  3 --> d2e300e1-7789-4dab-ae9b-62f7bf8131c9;
  style d2e300e1-7789-4dab-ae9b-62f7bf8131c9 stroke:#2c3143,stroke-width:4px;
  4["Bakta"];
  0 -->|output| 4;
  ba06e653-ec00-47e6-b3a3-ce4d7560a75f["Output\nbakta_annotation_summary"];
  4 --> ba06e653-ec00-47e6-b3a3-ce4d7560a75f;
  style ba06e653-ec00-47e6-b3a3-ce4d7560a75f stroke:#2c3143,stroke-width:4px;
  5["Bowtie2"];
  1 -->|output| 5;
  2 -->|output| 5;
  0 -->|output| 5;
  45a89727-fd73-400f-97c9-54640bd882e4["Output\nbowtie_mapping_stats"];
  5 --> 45a89727-fd73-400f-97c9-54640bd882e4;
  style 45a89727-fd73-400f-97c9-54640bd882e4 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;
  2819c19d-f742-47c5-abf3-dbb0e1b45779["Output\njbrowse_output"];
  8 --> 2819c19d-f742-47c5-abf3-dbb0e1b45779;
  style 2819c19d-f742-47c5-abf3-dbb0e1b45779 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: