Workflows

These workflows are associated with Clustering 3K PBMCs 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.

Clustering 3k PBMC with Scanpy
Bérénice Batut, Hans-Rudolf Hotz, Mehmet Tekman, Pavankumar Videm

Last updated Nov 21, 2023

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

flowchart TD
  0["ℹ️ Input Dataset\nBarcodes"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nGenes"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nMatrix"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nmito header"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Import Anndata and loom"];
  2 -->|output| 4;
  0 -->|output| 4;
  1 -->|output| 4;
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  4 -->|anndata| 9;
  10["Inspect AnnData"];
  8 -->|anndata_out| 10;
  11["Select last"];
  10 -->|var| 11;
  12["Text reformatting"];
  11 -->|outfile| 12;
  13["Search in textfiles"];
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  14["Replace Text"];
  12 -->|outfile| 14;
  15["Concatenate datasets"];
  3 -->|output| 15;
  14 -->|outfile| 15;
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  16 -->|anndata| 18;
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  28["Filter"];
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  30["Plot"];
  28 -->|anndata_out| 30;
  31["Remove confounders"];
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  32["Inspect and manipulate"];
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  33["Cluster, infer trajectories and embed"];
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  38["Plot"];
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  39["Cluster, infer trajectories and embed"];
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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 galaxy-upload 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: