Workflows

These workflows are associated with Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data

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.

Genome Assembly of MRSA using Illumina MiSeq Data
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 Europe Galaxy Australia Galaxy Main Galaxy France Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Dataset\nDRR187559_2"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nDRR187559_1"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["FastQC"];
  0 -->|output| 2;
  3["fastp"];
  1 -->|output| 3;
  0 -->|output| 3;
  a4112dac-647e-46d4-a0a7-94bfbb0bfaa7["Output\nfastp_json"];
  3 --> a4112dac-647e-46d4-a0a7-94bfbb0bfaa7;
  style a4112dac-647e-46d4-a0a7-94bfbb0bfaa7 stroke:#2c3143,stroke-width:4px;
  4["FastQC"];
  1 -->|output| 4;
  5["Shovill"];
  3 -->|out1| 5;
  3 -->|out2| 5;
  7ea3f737-240e-4059-b624-ea5457cd87be["Output\nshovill_log"];
  5 --> 7ea3f737-240e-4059-b624-ea5457cd87be;
  style 7ea3f737-240e-4059-b624-ea5457cd87be stroke:#2c3143,stroke-width:4px;
  6["Quast"];
  5 -->|contigs| 6;
  13822e2c-4c7f-470d-a638-559abbd35b30["Output\nquast_output"];
  6 --> 13822e2c-4c7f-470d-a638-559abbd35b30;
  style 13822e2c-4c7f-470d-a638-559abbd35b30 stroke:#2c3143,stroke-width:4px;
  7["Bandage Image"];
  5 -->|contigs_graph| 7;
  8["Bandage Info"];
  5 -->|contigs_graph| 8;
  0066ffc2-4639-414f-87fd-a7ed796df2c6["Output\nbandage_info_output"];
  8 --> 0066ffc2-4639-414f-87fd-a7ed796df2c6;
  style 0066ffc2-4639-414f-87fd-a7ed796df2c6 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:

Video: Importing a workflow from URL