Workflows

These workflows are associated with Metatranscriptomics analysis using microbiome RNA-seq 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.

Main Metatranscriptomics Analysis
Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep

Last updated Jan 11, 2024

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

Download Galaxy Workflow.ga Galaxy Main Galaxy Europe Galaxy France Galaxy Australia Import to another server (≥23.0+ only!) 
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;

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: