Workflows

These workflows are associated with Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina 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 Oxford Nanopore MinION (and Illumina data if available)
Bazante Sanders, Bérénice Batut

Last updated Feb 29, 2024

Launch in Tutorial Mode question
License: MIT
Tests: ✅ Results: Not yet automated

flowchart TD
  0["ℹ️ Input Dataset\nNanopore raw reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nIllumina forward raw reads"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nIllumina reverse raw reads"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Convert compressed file to uncompressed."];
  0 -->|output| 3;
  4["FastQC"];
  0 -->|output| 4;
  5["fastp"];
  1 -->|output| 5;
  2 -->|output| 5;
  6["NanoPlot"];
  3 -->|output1| 6;
  a97e6f33-8182-4a33-86dd-6cfbb83a842d["Output\nnanoplot_before_filtering"];
  6 --> a97e6f33-8182-4a33-86dd-6cfbb83a842d;
  style a97e6f33-8182-4a33-86dd-6cfbb83a842d stroke:#2c3143,stroke-width:4px;
  7["filtlong"];
  5 -->|out1| 7;
  5 -->|out2| 7;
  0 -->|output| 7;
  8["Flye"];
  7 -->|outfile| 8;
  f12e718f-1bd5-490d-bd41-f0747aaa41a6["Output\nflye_assembly_info"];
  8 --> f12e718f-1bd5-490d-bd41-f0747aaa41a6;
  style f12e718f-1bd5-490d-bd41-f0747aaa41a6 stroke:#2c3143,stroke-width:4px;
  9["NanoPlot"];
  7 -->|outfile| 9;
  89524090-f590-434d-89e2-66f0b1a23c7c["Output\nnanoplot_after_filtering"];
  9 --> 89524090-f590-434d-89e2-66f0b1a23c7c;
  style 89524090-f590-434d-89e2-66f0b1a23c7c stroke:#2c3143,stroke-width:4px;
  10["Bandage Image"];
  8 -->|assembly_gfa| 10;
  11["BWA-MEM2"];
  5 -->|out2| 11;
  8 -->|consensus| 11;
  12["Quast"];
  8 -->|consensus| 12;
  dabfb8fd-8791-4959-a9dc-9b3c1e57a69c["Output\nquast_report_before_polishing"];
  12 --> dabfb8fd-8791-4959-a9dc-9b3c1e57a69c;
  style dabfb8fd-8791-4959-a9dc-9b3c1e57a69c stroke:#2c3143,stroke-width:4px;
  13["BWA-MEM2"];
  5 -->|out1| 13;
  8 -->|consensus| 13;
  14["Polypolish"];
  8 -->|consensus| 14;
  13 -->|bam_output| 14;
  11 -->|bam_output| 14;
  15["Quast"];
  14 -->|polished_fasta| 15;
  8 -->|consensus| 15;
  4e465b51-68bf-4203-9a7c-897f46c70277["Output\nquast_report_after_polishing"];
  15 --> 4e465b51-68bf-4203-9a7c-897f46c70277;
  style 4e465b51-68bf-4203-9a7c-897f46c70277 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