Main Metatranscriptomics Analysis

microbiome-metatranscriptomics/main-workflow

Author(s)
Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep
Version
1
Last updated
Jan 11, 2024
License
MIT
Tags

Features
Tutorial
Metatranscriptomics analysis using microbiome RNA-seq data
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00127
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nT1A_forward"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nT1A_reverse"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["🛠️ Subworkflow\nWorkflow 1: Preprocessing"];
  style 2 fill:#edd,stroke:#900,stroke-width:4px;
  0 -->|output| 2;
  1 -->|output| 2;
  3["🛠️ Subworkflow\nWorkflow 2: Community Profile"];
  style 3 fill:#edd,stroke:#900,stroke-width:4px;
  2 -->|Cutadapt on input datasets: Read 1 Output| 3;
  2 -->|Cutadapt on input datasets: Read 2 Output| 3;
  4["🛠️ Subworkflow\nWorkflow 3: Functional Information"];
  style 4 fill:#edd,stroke:#900,stroke-width:4px;
  2 -->|FASTQ interlacer pairs from input datasets| 4;
  3 -->|MetaPhlAn on input datasets: Predicted taxon relative abundances| 4;

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/metatranscriptomics/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