Taxonomic Profiling and Visualization of Metagenomic Data

microbiome-taxonomic-profiling/main-workflow

Author(s)
Bérénice Batut
Version
1
Last updated
Jan 15, 2024
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;
  e6c6a211-f878-417a-b7f8-488bbce5efa2["Output\nkraken_report"];
  3 --> e6c6a211-f878-417a-b7f8-488bbce5efa2;
  style e6c6a211-f878-417a-b7f8-488bbce5efa2 stroke:#2c3143,stroke-width:4px;
  4["MetaPhlAn"];
  2 -->|forward| 4;
  2 -->|reverse| 4;
  e46a3b2e-039e-41ff-8fc6-d4fdc6849edb["Output\nmetaphlan_output"];
  4 --> e46a3b2e-039e-41ff-8fc6-d4fdc6849edb;
  style e46a3b2e-039e-41ff-8fc6-d4fdc6849edb stroke:#2c3143,stroke-width:4px;
  5["Krakentools: Convert kraken report file"];
  3 -->|report_output| 5;
  e69aeae5-6a04-41dc-9bc8-1e21eddf49a4["Output\nkrakentool_report"];
  5 --> e69aeae5-6a04-41dc-9bc8-1e21eddf49a4;
  style e69aeae5-6a04-41dc-9bc8-1e21eddf49a4 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;

Inputs

Input Label
raw-reads raw-reads
metadata metadata

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1 Kraken2
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.6+galaxy1 MetaPhlAn
toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy0 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/2.7+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+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+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.6+galaxy1 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
  • 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

Version History

Version Commit Time Comments
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