Cell Cycle Regression Workflow

Run Workflow in Galaxy

• Galaxy Main
• Galaxy Australia
• Galaxy France
• Galaxy Europe
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nAnnData After QC, normalisation, scaling"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nS Phase Genes"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nG2M Phase Genes"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nPasted Entry"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Inspect AnnData"];
  0 -->|output| 4;
  5["All Cell Cycle Genes Concatenate S and G2M Genes"];
  1 -->|output| 5;
  2 -->|output| 5;
  6["Inspect and manipulate"];
  0 -->|output| 6;
  2 -->|output| 6;
  1 -->|output| 6;
  7["Table Compute"];
  4 -->|var| 7;
  8["Add column"];
  5 -->|out_file1| 8;
  9["Scanpy RegressOut"];
  6 -->|anndata_out| 9;
  026b02d3-97ee-4847-9347-40773ab76356["Output\nScanpy RegressOut on input dataset(s): Regressed out  AnnData"];
  9 --> 026b02d3-97ee-4847-9347-40773ab76356;
  style 026b02d3-97ee-4847-9347-40773ab76356 stroke:#2c3143,stroke-width:4px;
  10["Add column"];
  7 -->|table| 10;
  11["Join"];
  10 -->|out_file1| 11;
  8 -->|out_file1| 11;
  12["Sort"];
  11 -->|output| 12;
  13["Table Compute"];
  12 -->|out_file1| 13;
  14["Concatenate datasets"];
  3 -->|output| 14;
  13 -->|table| 14;
  15["Manipulate AnnData"];
  6 -->|anndata_out| 15;
  14 -->|out_file1| 15;
  16["Manipulate AnnData"];
  9 -->|output_h5ad| 16;
  14 -->|out_file1| 16;
  17["Manipulate AnnData"];
  15 -->|anndata| 17;
  18["Manipulate AnnData"];
  16 -->|anndata| 18;
  19["Cluster, infer trajectories and embed"];
  17 -->|anndata| 19;
  20["Cluster, infer trajectories and embed"];
  18 -->|anndata| 20;
  09d97ef7-ed92-4d90-a597-2032581c2d4a["Output\nCluster, infer trajectories and embed (tl.louvain) on input dataset(s): Annotated data matrix"];
  20 --> 09d97ef7-ed92-4d90-a597-2032581c2d4a;
  style 09d97ef7-ed92-4d90-a597-2032581c2d4a stroke:#2c3143,stroke-width:4px;
  21["Plot"];
  19 -->|anndata_out| 21;
  22["Plot"];
  20 -->|anndata_out| 22;

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

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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_cell-cycle/workflows/main_workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows