Workflows

These workflows are associated with Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution

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["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;
	

flowchart TD
  0["EBI SCXA Data Retrieval"];
  1["Cut"];
  0 -->|design_tsv| 1;
  2["Add line to file"];
  0 -->|barcode_tsv| 2;
  3["Reformatting metadata columns"];
  1 -->|out_file1| 3;
  4["Join two Datasets"];
  2 -->|outfile| 4;
  3 -->|out_file1| 4;
  5["Advanced Cut"];
  4 -->|out_file1| 5;
	

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: