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;
  ff5c579d-a34c-4e9a-8c28-dcc414a6428a["Output\nkraken_report"];
  4 --> ff5c579d-a34c-4e9a-8c28-dcc414a6428a;
  style ff5c579d-a34c-4e9a-8c28-dcc414a6428a 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;
  a60f19b9-c1ae-4109-ad92-d8e24ac20aeb["Output\nkrakentool_report"];
  7 --> a60f19b9-c1ae-4109-ad92-d8e24ac20aeb;
  style a60f19b9-c1ae-4109-ad92-d8e24ac20aeb 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: