Workflows

These workflows are associated with Taxonomic Profiling and Visualization of Metagenomic 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.

Taxonomic Profiling and Visualization of Metagenomic Data

Bérénice Batut

Last updated Jan 15, 2024

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

flowchart TD
  0["ℹ️ Input Collection\nraw-reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nmetadata"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Unzip collection"];
  0 -->|output| 2;
  3["Kraken2"];
  0 -->|output| 3;
  2007fe3f-e3f2-40ba-a02d-8130d997ee5f["Output\nkraken_report"];
  3 --> 2007fe3f-e3f2-40ba-a02d-8130d997ee5f;
  style 2007fe3f-e3f2-40ba-a02d-8130d997ee5f stroke:#2c3143,stroke-width:4px;
  4["MetaPhlAn"];
  2 -->|forward| 4;
  2 -->|reverse| 4;
  464e955d-0bb5-475e-9878-c0a0a41969b4["Output\nmetaphlan_output"];
  4 --> 464e955d-0bb5-475e-9878-c0a0a41969b4;
  style 464e955d-0bb5-475e-9878-c0a0a41969b4 stroke:#2c3143,stroke-width:4px;
  5["Krakentools: Convert kraken report file"];
  3 -->|report_output| 5;
  1195fbf7-4187-48ed-8738-6712844e04f9["Output\nkrakentool_report"];
  5 --> 1195fbf7-4187-48ed-8738-6712844e04f9;
  style 1195fbf7-4187-48ed-8738-6712844e04f9 stroke:#2c3143,stroke-width:4px;
  6["Kraken-biom"];
  3 -->|report_output| 6;
  1 -->|output| 6;
  7["Pavian"];
  3 -->|report_output| 7;
  8["Estimate Abundance at Taxonomic Level"];
  3 -->|report_output| 8;
  9["Krona pie chart"];
  4 -->|krona_output_file| 9;
  10["Krona pie chart"];
  5 -->|output| 10;
  11["Phinch Visualisation"];
  6 -->|biomOutput| 11;

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