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

flowchart TD
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  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;
  552ddee1-9559-4aaa-8354-08f55ee2e255["Output\nfastp_json"];
  3 --> 552ddee1-9559-4aaa-8354-08f55ee2e255;
  style 552ddee1-9559-4aaa-8354-08f55ee2e255 stroke:#2c3143,stroke-width:4px;
  4["FastQC"];
  1 -->|output| 4;
  5["Shovill"];
  3 -->|out1| 5;
  3 -->|out2| 5;
  9baa74ed-6116-46d2-a45c-d77240b893d3["Output\nshovill_log"];
  5 --> 9baa74ed-6116-46d2-a45c-d77240b893d3;
  style 9baa74ed-6116-46d2-a45c-d77240b893d3 stroke:#2c3143,stroke-width:4px;
  6["Quast"];
  5 -->|contigs| 6;
  24f61832-40fe-4523-bc03-98bca2163ab0["Output\nquast_output"];
  6 --> 24f61832-40fe-4523-bc03-98bca2163ab0;
  style 24f61832-40fe-4523-bc03-98bca2163ab0 stroke:#2c3143,stroke-width:4px;
  7["Bandage Image"];
  5 -->|contigs_graph| 7;
  8["Bandage Info"];
  5 -->|contigs_graph| 8;
  ad4dd10f-ebc8-4037-b2ca-b59fa1b4c137["Output\nbandage_info_output"];
  8 --> ad4dd10f-ebc8-4037-b2ca-b59fa1b4c137;
  style ad4dd10f-ebc8-4037-b2ca-b59fa1b4c137 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: