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
License: MIT
Tests: ✅ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy Main Galaxy Australia Galaxy Europe Galaxy France Import to another server (≥23.0+ only!) 
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;
  e892f29c-7f9f-470d-b23b-a2f436a8307f["Output\nkraken_report"];
  3 --> e892f29c-7f9f-470d-b23b-a2f436a8307f;
  style e892f29c-7f9f-470d-b23b-a2f436a8307f stroke:#2c3143,stroke-width:4px;
  4["MetaPhlAn"];
  2 -->|forward| 4;
  2 -->|reverse| 4;
  aadcd770-3455-4011-85e1-aa48cd3f93c6["Output\nmetaphlan_output"];
  4 --> aadcd770-3455-4011-85e1-aa48cd3f93c6;
  style aadcd770-3455-4011-85e1-aa48cd3f93c6 stroke:#2c3143,stroke-width:4px;
  5["Krakentools: Convert kraken report file"];
  3 -->|report_output| 5;
  30346843-eed2-4f22-8f1d-4d79c7d7e996["Output\nkrakentool_report"];
  5 --> 30346843-eed2-4f22-8f1d-4d79c7d7e996;
  style 30346843-eed2-4f22-8f1d-4d79c7d7e996 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 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