Workflows

These workflows are associated with Converting between common single cell data formats

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.

flowchart TD
  0["ℹ️ Input Dataset\nAnnData"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Inspect AnnData"];
  0 -->|output| 1;
  7bdb825c-6a89-4a34-bbd9-a79c309c9750["Output\nInspect AnnData: obs"];
  1 --> 7bdb825c-6a89-4a34-bbd9-a79c309c9750;
  style 7bdb825c-6a89-4a34-bbd9-a79c309c9750 stroke:#2c3143,stroke-width:4px;
  2["Inspect AnnData"];
  0 -->|output| 2;
  79a2e3e5-4bd6-42de-864c-a5dc2412cb86["Output\nInspect AnnData: var"];
  2 --> 79a2e3e5-4bd6-42de-864c-a5dc2412cb86;
  style 79a2e3e5-4bd6-42de-864c-a5dc2412cb86 stroke:#2c3143,stroke-width:4px;
  3["Inspect AnnData"];
  0 -->|output| 3;
  7a254954-7e32-4e8a-bd4c-a79abf9db8d8["Output\nInspect AnnData: X"];
  3 --> 7a254954-7e32-4e8a-bd4c-a79abf9db8d8;
  style 7a254954-7e32-4e8a-bd4c-a79abf9db8d8 stroke:#2c3143,stroke-width:4px;
  4["Transpose"];
  3 -->|X| 4;
  5["Monocle3 create"];
  1 -->|obs| 5;
  4 -->|out_file| 5;
  2 -->|var| 5;
  6bf4a0ea-3cb9-470c-9863-0a7eb0bc3d8c["Output\nCDS Monocle file"];
  5 --> 6bf4a0ea-3cb9-470c-9863-0a7eb0bc3d8c;
  style 6bf4a0ea-3cb9-470c-9863-0a7eb0bc3d8c stroke:#2c3143,stroke-width:4px;
	

flowchart TD
  0["ℹ️ Input Dataset\nAnnData"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Inspect AnnData"];
  0 -->|output| 1;
  6d03d713-8d71-4f6a-9f83-cd999f423ebf["Output\nInspect AnnData: obs"];
  1 --> 6d03d713-8d71-4f6a-9f83-cd999f423ebf;
  style 6d03d713-8d71-4f6a-9f83-cd999f423ebf stroke:#2c3143,stroke-width:4px;
  2["Inspect AnnData"];
  0 -->|output| 2;
  ea025a8a-6f3a-4e38-a3af-db406886c7de["Output\nInspect AnnData: X"];
  2 --> ea025a8a-6f3a-4e38-a3af-db406886c7de;
  style ea025a8a-6f3a-4e38-a3af-db406886c7de stroke:#2c3143,stroke-width:4px;
  3["Transpose"];
  2 -->|X| 3;
  4["DropletUtils"];
  3 -->|out_file| 4;
  5["Seurat Read10x"];
  4 -->|barcodes_out| 5;
  4 -->|genes_out| 5;
  4 -->|matrix_out| 5;
  1 -->|obs| 5;
  e5fec5dc-4706-48e5-8326-05e70290552d["Output\nConverted Seurat object"];
  5 --> e5fec5dc-4706-48e5-8326-05e70290552d;
  style e5fec5dc-4706-48e5-8326-05e70290552d stroke:#2c3143,stroke-width:4px;
	

flowchart TD
  0["ℹ️ Input Dataset\nAnnData"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Parameter\nCell ID column"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["Inspect AnnData"];
  0 -->|output| 2;
  8b9200c2-96e6-40fa-a8e9-1e99638c733f["Output\nInspect AnnData: obs"];
  2 --> 8b9200c2-96e6-40fa-a8e9-1e99638c733f;
  style 8b9200c2-96e6-40fa-a8e9-1e99638c733f stroke:#2c3143,stroke-width:4px;
  3["Inspect AnnData"];
  0 -->|output| 3;
  9fc4ce5a-8384-484d-b1cd-c0f5137cf821["Output\nInspect AnnData: X"];
  3 --> 9fc4ce5a-8384-484d-b1cd-c0f5137cf821;
  style 9fc4ce5a-8384-484d-b1cd-c0f5137cf821 stroke:#2c3143,stroke-width:4px;
  4["Transpose"];
  3 -->|X| 4;
  5["DropletUtils"];
  4 -->|out_file| 5;
  6["DropletUtils Read10x"];
  1 -->|output| 6;
  2 -->|obs| 6;
  5 -->|barcodes_out| 6;
  5 -->|genes_out| 6;
  5 -->|matrix_out| 6;
  3256e23f-2026-407d-aa25-0f8c0f3ae3f7["Output\nConverted SCE object"];
  6 --> 3256e23f-2026-407d-aa25-0f8c0f3ae3f7;
  style 3256e23f-2026-407d-aa25-0f8c0f3ae3f7 stroke:#2c3143,stroke-width:4px;
	

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: