Workflows

These workflows are associated with Identification of the micro-organisms in a beer using Nanopore sequencing

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.

Identification of the micro-organisms in a beer using Nanopore sequencing
Bérénice Batut, Teresa Müller, Polina Polunina

Last updated Jan 11, 2024

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

flowchart TD
  0["ℹ️ Input Dataset\ninput"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["FastQC"];
  0 -->|output| 1;
  2["Porechop"];
  0 -->|output| 2;
  3["fastp"];
  2 -->|outfile| 3;
  4["Kraken2"];
  3 -->|out1| 4;
  0ce2508d-419a-42e6-9182-fdc5e9328e45["Output\nkraken_report"];
  4 --> 0ce2508d-419a-42e6-9182-fdc5e9328e45;
  style 0ce2508d-419a-42e6-9182-fdc5e9328e45 stroke:#2c3143,stroke-width:4px;
  5["Filter"];
  4 -->|report_output| 5;
  6["Filter"];
  4 -->|report_output| 6;
  7["Krakentools: Convert kraken report file"];
  4 -->|report_output| 7;
  650a8246-c9ef-4073-85fc-8361be9b4a2e["Output\nkrakentool_report"];
  7 --> 650a8246-c9ef-4073-85fc-8361be9b4a2e;
  style 650a8246-c9ef-4073-85fc-8361be9b4a2e stroke:#2c3143,stroke-width:4px;
  8["Krona pie chart"];
  7 -->|output| 8;
	

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: