Workflows

These workflows are associated with Inferring single cell trajectories with Scanpy

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.

Inferring Trajectories with Scanpy Tutorial Workflow
Marisa Loach

Last updated Dec 8, 2023

Launch in Tutorial Mode
License: CC-BY-4.0
Tests: ✅ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy Europe Galaxy Australia Galaxy Main Galaxy France Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Dataset\nInput Anndata"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Manipulate AnnData"];
  0 -->|output| 1;
  2["Scanpy RunFDG"];
  1 -->|anndata| 2;
  3["Scanpy PlotEmbed"];
  2 -->|output_h5ad| 3;
  4["Scanpy DiffusionMap"];
  2 -->|output_h5ad| 4;
  5["Scanpy ComputeGraph"];
  4 -->|output_h5ad| 5;
  6["Scanpy RunFDG"];
  5 -->|output_h5ad| 6;
  7["Scanpy PlotEmbed"];
  6 -->|output_h5ad| 7;
  8["Scanpy PAGA"];
  6 -->|output_h5ad| 8;
  9["Scanpy PlotTrajectory"];
  8 -->|output_h5ad| 9;
  10["Scanpy RunFDG"];
  9 -->|output_h5ad| 10;
  11["Scanpy PlotEmbed"];
  10 -->|output_h5ad| 11;
  12["Scanpy PlotEmbed"];
  10 -->|output_h5ad| 12;
  13["Scanpy PlotEmbed"];
  10 -->|output_h5ad| 13;
  14["Final Anndata with Trajectory and DPT"];
  10 -->|output_h5ad| 14;
  15["Scanpy PlotEmbed"];
  14 -->|output_h5ad| 15;

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