flowchart TD
0["EBI SCXA Data Retrieval"];
1["ℹ️ Input Dataset\nSingle cell metadata"];
style 1 stroke:#2c3143,stroke-width:4px;
2["Scanpy Read10x"];
0 -->|barcode_tsv| 2;
0 -->|genes_tsv| 2;
0 -->|matrix_mtx| 2;
6bd01730-f0b5-4824-8cfc-d563cc9c7f7d["Output\nScanpy Read10x on input dataset(s): anndata"];
2 --> 6bd01730-f0b5-4824-8cfc-d563cc9c7f7d;
style 6bd01730-f0b5-4824-8cfc-d563cc9c7f7d stroke:#2c3143,stroke-width:4px;
3["Inspect AnnData"];
2 -->|output_h5| 3;
4["Transpose"];
3 -->|X| 4;
5["annotateMyIDs"];
4 -->|out_file| 5;
c39c7d69-550e-4b54-a412-317b599c5e55["Output\nannotateMyIDs on input dataset(s): Annotated IDs"];
5 --> c39c7d69-550e-4b54-a412-317b599c5e55;
style c39c7d69-550e-4b54-a412-317b599c5e55 stroke:#2c3143,stroke-width:4px;
6["🛠️ Subworkflow\n1st step removed - Convert from Ensembl to GeneSymbol, summing duplicate genes"];
style 6 fill:#edd,stroke:#900,stroke-width:4px;
5 -->|out_tab| 6;
4 -->|out_file| 6;
7["Construct Expression Set Object"];
6 -->|Gene Symbol Count Matrix| 7;
1 -->|output| 7;
e8c91df0-4e6c-4eb2-9807-c2679b494958["Output\nConstruct Expression Set Object on input dataset(s): RData ESet Object"];
7 --> e8c91df0-4e6c-4eb2-9807-c2679b494958;
style e8c91df0-4e6c-4eb2-9807-c2679b494958 stroke:#2c3143,stroke-width:4px;
2912d09b-b178-4035-b7c8-7038392e2bf2["Output\nConstruct Expression Set Object on input dataset(s): General Info"];
7 --> 2912d09b-b178-4035-b7c8-7038392e2bf2;
style 2912d09b-b178-4035-b7c8-7038392e2bf2 stroke:#2c3143,stroke-width:4px;
8["Manipulate Expression Set Object"];
7 -->|out_rds| 8;
08de92d8-32fe-4b47-9038-298cdd13fac5["Output\nManipulate Expression Set Object on input dataset(s): ExpressionSet Object"];
8 --> 08de92d8-32fe-4b47-9038-298cdd13fac5;
style 08de92d8-32fe-4b47-9038-298cdd13fac5 stroke:#2c3143,stroke-width:4px;
9["Manipulate Expression Set Object"];
7 -->|out_rds| 9;
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
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 galaxy-uploadImport 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:
Download Workflow RO-Crate
View on WorkflowHub