LOCKED | Combining single cell datasets after pre-processing

Run Workflow in Galaxy

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• Import to another server (≥23.0+ only!)

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  1["ℹ️ Input Dataset\nSample 2"];
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  4["ℹ️ Input Dataset\nSample 5"];
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  5["ℹ️ Input Dataset\nSample 6"];
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  6["ℹ️ Input Dataset\nSample 7"];
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  7["Combined_Object"];
  0 -->|output| 7;
  1 -->|output| 7;
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  3 -->|output| 7;
  4 -->|output| 7;
  5 -->|output| 7;
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  7 -->|anndata| 10;
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  11["Generating sex metadata"];
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  12["Generating genotype metadata"];
  10 -->|obs| 12;
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  15["Cell_Metadata"];
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  18["Inspect AnnData"];
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Inputs

Outputs

Tools

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

Hands On: Importing a workflow

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. 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”
4. Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/workflows/Combining_single_cell_datasets_after_pre-processing.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