Combining datasets after pre-processing

Run Workflow in Galaxy

• Galaxy Europe
• Galaxy Australia
• Galaxy Main
• Galaxy France
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nN701"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nN702"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nN703"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nN704"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nN705"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nN706"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["ℹ️ Input Dataset\nN707"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["Concatenating Datasets"];
  0 -->|output| 7;
  1 -->|output| 7;
  2 -->|output| 7;
  3 -->|output| 7;
  4 -->|output| 7;
  5 -->|output| 7;
  6 -->|output| 7;
  168d4710-570a-43b1-998a-2164154eebc5["Output\nCombined Object"];
  7 --> 168d4710-570a-43b1-998a-2164154eebc5;
  style 168d4710-570a-43b1-998a-2164154eebc5 stroke:#2c3143,stroke-width:4px;
  8["Inspect AnnData"];
  7 -->|anndata| 8;
  9["Inspect AnnData"];
  7 -->|anndata| 9;
  10["Inspect AnnData"];
  7 -->|anndata| 10;
  11["Replace Text"];
  9 -->|obs| 11;
  12["Replace Text"];
  9 -->|obs| 12;
  13["Cut"];
  11 -->|outfile| 13;
  8b026c35-f9db-4bcd-8cf5-54b7d6fb5aea["Output\nSex metadata"];
  13 --> 8b026c35-f9db-4bcd-8cf5-54b7d6fb5aea;
  style 8b026c35-f9db-4bcd-8cf5-54b7d6fb5aea stroke:#2c3143,stroke-width:4px;
  14["Cut"];
  12 -->|outfile| 14;
  6f55548b-5ded-42b8-b2f7-c7f1a327a068["Output\nGenotype metadata"];
  14 --> 6f55548b-5ded-42b8-b2f7-c7f1a327a068;
  style 6f55548b-5ded-42b8-b2f7-c7f1a327a068 stroke:#2c3143,stroke-width:4px;
  15["Paste"];
  14 -->|out_file1| 15;
  13 -->|out_file1| 15;
  2f0ea0f3-f2f7-44b2-b8f0-05d8cbb364a6["Output\nCell metadata"];
  15 --> 2f0ea0f3-f2f7-44b2-b8f0-05d8cbb364a6;
  style 2f0ea0f3-f2f7-44b2-b8f0-05d8cbb364a6 stroke:#2c3143,stroke-width:4px;
  16["Adding in cell metadata"];
  7 -->|anndata| 16;
  15 -->|out_file1| 16;
  2720386c-7273-49d6-abb0-9bd14f6cb68c["Output\nAnnData with Cell Metadata"];
  16 --> 2720386c-7273-49d6-abb0-9bd14f6cb68c;
  style 2720386c-7273-49d6-abb0-9bd14f6cb68c stroke:#2c3143,stroke-width:4px;
  17["Batching Cell Metadata"];
  16 -->|anndata| 17;
  b950c8db-abe1-4cb0-af58-d291d3b74a83["Output\nBatched Object"];
  17 --> b950c8db-abe1-4cb0-af58-d291d3b74a83;
  style b950c8db-abe1-4cb0-af58-d291d3b74a83 stroke:#2c3143,stroke-width:4px;
  18["Calculating mitochondrial "];
  17 -->|anndata| 18;
  2417284d-8252-43ff-84bf-6f15ef11cd05["Output\nAnnotated AnnData"];
  18 --> 2417284d-8252-43ff-84bf-6f15ef11cd05;
  style 2417284d-8252-43ff-84bf-6f15ef11cd05 stroke:#2c3143,stroke-width:4px;

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

• 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:

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-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