GO Enrichment Workflow

single-cell-GO-enrichment/main-workflow

Author(s)
Menna Gamal
Version
1
Last updated
Sep 17, 2024
License
CC-BY-4.0
Tags

Features
Tutorial
GO Enrichment Analysis on Single-Cell RNA-Seq Data
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00287
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 Dataset\nMarker Genes"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nGO"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nAnnotation"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nBackground"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Split file"];
  0 -->|output| 4;
  5["Cut"];
  4 -->|split_output| 5;
  6["GOEnrichment"];
  2 -->|output| 6;
  1 -->|output| 6;
  3 -->|output| 6;
  5 -->|out_file1| 6;
  7["gProfiler GOSt"];
  5 -->|out_file1| 7;

Inputs

Input Label
Input dataset Marker Genes
Input dataset GO
Input dataset Annotation
Input dataset Background

Outputs

From Output Label

Tools

Tool Links
Cut1
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/goenrichment/goenrichment/2.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/gprofiler_gost/gprofiler_gost/0.1.7+galaxy11 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
5 2d8afbe27 2024-09-13 13:28:30 Update main_workflow.ga
4 8b5a810af 2024-09-13 11:08:25 Update main_workflow.ga
3 627cef42b 2024-09-13 09:55:46 Update main_workflow.ga
2 53a1b9f1b 2024-09-13 09:46:05 Update main_workflow.ga
1 0093a305a 2024-08-29 09:32:49 adding files

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/GO-enrichment/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