Taxonomic Profiling and Visualization of Metagenomic Data

microbiome-taxonomic-profiling/main-workflow

Author(s)
Bérénice Batut, Tarnima Omara
Version
2
Last updated
Apr 4, 2025
License
MIT
Tags
microbiome

Features
Tutorial
Taxonomic Profiling and Visualization of Metagenomic Data
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00147
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
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;
  4["MetaPhlAn"];
  2 -->|forward| 4;
  2 -->|reverse| 4;
  9affde3b-b159-486e-bb38-c628ac72e7fc["Output\nmetaphlan_output"];
  4 --> 9affde3b-b159-486e-bb38-c628ac72e7fc;
  style 9affde3b-b159-486e-bb38-c628ac72e7fc stroke:#2c3143,stroke-width:4px;
  5["Krakentools: Convert kraken report file"];
  3 -->|report_output| 5;
  b14415d5-66e2-4f79-89d6-ae0bcd837796["Output\nkrakentool_report"];
  5 --> b14415d5-66e2-4f79-89d6-ae0bcd837796;
  style b14415d5-66e2-4f79-89d6-ae0bcd837796 stroke:#2c3143,stroke-width:4px;
  6["Kraken-biom"];
  3 -->|report_output| 6;
  1 -->|output| 6;
  7["Pavian"];
  3 -->|report_output| 7;
  8["Bracken"];
  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;

Inputs

Input Label
Input dataset collection raw-reads
Input dataset metadata

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy4 MetaPhlAn
toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy2 Krakentools: Convert kraken report file

Tools

Tool Links
__UNZIP_COLLECTION__
interactive_tool_pavian
interactive_tool_phinch
toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/kraken_biom/kraken_biom/1.2.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy4 View in ToolShed

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.

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
  1. Click on Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on Import at the top-right of the screen
  3. 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”
  4. 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

Version History

Version Commit Time Comments
4 dde205039 2025-04-03 23:11:42 Update topics/microbiome/tutorials/taxonomic-profiling/workflows/main-workflow.ga
3 364bb343b 2025-04-03 23:09:54 Update topics/microbiome/tutorials/taxonomic-profiling/workflows/main-workflow.ga
2 2159350d9 2025-04-03 02:28:29 Update main-workflow.ga
1 0e0a2f2cc 2024-01-10 15:47:09 Rename metagenomics topic to microbiome

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/taxonomic-profiling/workflows/main-workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows