Workflows

These workflows are associated with Importing files from public atlases

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.

EBI SCXA to AnnData (Scanpy) or Seurat Object
Julia Jakiela

Last updated Dec 14, 2023

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

Download Galaxy Workflow.ga Galaxy Europe Galaxy Main Galaxy France Galaxy Australia Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Parameter\nSC-Atlas experiment accession"];
  style 0 fill:#ded,stroke:#393,stroke-width:4px;
  1["EBI SCXA Data Retrieval"];
  0 -->|output| 1;
  2["Rename batch numbers"];
  1 -->|design_tsv| 2;
  3["Mito genes check"];
  1 -->|genes_tsv| 3;
  b0762cfd-58bd-4c39-ae41-2dca4289c541["Output\nMito genes check"];
  3 --> b0762cfd-58bd-4c39-ae41-2dca4289c541;
  style b0762cfd-58bd-4c39-ae41-2dca4289c541 stroke:#2c3143,stroke-width:4px;
  4["Rename cell metadata headers"];
  2 -->|out_file1| 4;
  5["Create AnnData"];
  1 -->|barcode_tsv| 5;
  4 -->|outfile| 5;
  1 -->|genes_tsv| 5;
  1 -->|matrix_mtx| 5;
  938cd594-61cf-4037-a58b-c09c065db505["Output\nAnnData object"];
  5 --> 938cd594-61cf-4037-a58b-c09c065db505;
  style 938cd594-61cf-4037-a58b-c09c065db505 stroke:#2c3143,stroke-width:4px;
  6["Seurat Read10x"];
  1 -->|barcode_tsv| 6;
  1 -->|genes_tsv| 6;
  1 -->|matrix_mtx| 6;
  4 -->|outfile| 6;
  c24e9d83-c175-40a2-9c36-eeb486fe323e["Output\nSeurat object"];
  6 --> c24e9d83-c175-40a2-9c36-eeb486fe323e;
  style c24e9d83-c175-40a2-9c36-eeb486fe323e stroke:#2c3143,stroke-width:4px;
  7["AnnData Operations"];
  5 -->|output_h5ad| 7;
  b47f801f-bedb-4136-a5e9-378a815a1799["Output\nMito-counted AnnData for downstream analysis"];
  7 --> b47f801f-bedb-4136-a5e9-378a815a1799;
  style b47f801f-bedb-4136-a5e9-378a815a1799 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: