Workflows

These workflows are associated with Combining single cell datasets after pre-processing

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.

CS2_Combining datasets after pre-processing

Last updated Nov 12, 2022

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License: None Specified, defaults to CC-BY-4.0
Tests: ❌ Results: Not yet automated

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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["EBI SCXA Data Retrieval"];
  8["Concatenating Datasets"];
  0 -->|output| 8;
  1 -->|output| 8;
  2 -->|output| 8;
  3 -->|output| 8;
  4 -->|output| 8;
  5 -->|output| 8;
  6 -->|output| 8;
  a138b78c-0bab-476f-86ac-046e71f1ffd2["Output\nCombined AnnData"];
  8 --> a138b78c-0bab-476f-86ac-046e71f1ffd2;
  style a138b78c-0bab-476f-86ac-046e71f1ffd2 stroke:#2c3143,stroke-width:4px;
  9["Scanpy Read10x"];
  7 -->|barcode_tsv| 9;
  7 -->|design_tsv| 9;
  7 -->|genes_tsv| 9;
  7 -->|matrix_mtx| 9;
  cb74756e-46b8-428d-a642-0ac981ab7b96["Output\nScanpy Read10x on input dataset(s): anndata_h5ad AnnData"];
  9 --> cb74756e-46b8-428d-a642-0ac981ab7b96;
  style cb74756e-46b8-428d-a642-0ac981ab7b96 stroke:#2c3143,stroke-width:4px;
  10["Inspect AnnData"];
  8 -->|anndata| 10;
  11["Inspect AnnData"];
  8 -->|anndata| 11;
  12["Inspect AnnData"];
  8 -->|anndata| 12;
  13["Replace Text"];
  11 -->|obs| 13;
  14["Replace Text"];
  11 -->|obs| 14;
  15["Cut"];
  13 -->|outfile| 15;
  1added7f-58cd-4ad1-ac44-d033c7c7968e["Output\nSex metadata"];
  15 --> 1added7f-58cd-4ad1-ac44-d033c7c7968e;
  style 1added7f-58cd-4ad1-ac44-d033c7c7968e stroke:#2c3143,stroke-width:4px;
  16["Cut"];
  14 -->|outfile| 16;
  26e71b3f-663c-4249-8ca0-d3a8f69a437b["Output\nGenotype metadata"];
  16 --> 26e71b3f-663c-4249-8ca0-d3a8f69a437b;
  style 26e71b3f-663c-4249-8ca0-d3a8f69a437b stroke:#2c3143,stroke-width:4px;
  17["Paste"];
  16 -->|out_file1| 17;
  15 -->|out_file1| 17;
  60ff7e7d-004d-4d15-a2fb-876929ef539f["Output\nCell metadata"];
  17 --> 60ff7e7d-004d-4d15-a2fb-876929ef539f;
  style 60ff7e7d-004d-4d15-a2fb-876929ef539f stroke:#2c3143,stroke-width:4px;
  18["Adding in cell metadata"];
  8 -->|anndata| 18;
  17 -->|out_file1| 18;
  fb5f7421-77af-4a3a-8653-2302900c1786["Output\nAnnData with Cell Metadata"];
  18 --> fb5f7421-77af-4a3a-8653-2302900c1786;
  style fb5f7421-77af-4a3a-8653-2302900c1786 stroke:#2c3143,stroke-width:4px;
  19["Batching Cell Metadata"];
  18 -->|anndata| 19;
  30140d83-7b5f-48be-8e3b-f85acb8c278b["Output\nBatched AnnData"];
  19 --> 30140d83-7b5f-48be-8e3b-f85acb8c278b;
  style 30140d83-7b5f-48be-8e3b-f85acb8c278b stroke:#2c3143,stroke-width:4px;
  20["Calculating mitochondrial "];
  19 -->|anndata| 20;
  a6c9658e-e53d-4489-90d5-4f05af7a4c78["Output\nAnnotated AnnData"];
  20 --> a6c9658e-e53d-4489-90d5-4f05af7a4c78;
  style a6c9658e-e53d-4489-90d5-4f05af7a4c78 stroke:#2c3143,stroke-width:4px;

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: