Music Stage 2 - Inferring cellular proportions

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Collection\nPseudobulk - A"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nPseudobulk - B"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Collection\nESet Reference scRNA-seq"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Parameter\nCell Types Label from scRNA dataset"];
  style 3 fill:#ded,stroke:#393,stroke-width:4px;
  4["ℹ️ Input Parameter\nSamples Identifer from scRNA dataset"];
  style 4 fill:#ded,stroke:#393,stroke-width:4px;
  5["ℹ️ Input Parameter\nCell types to use from scRNA dataset"];
  style 5 fill:#ded,stroke:#393,stroke-width:4px;
  6["ℹ️ Input Collection\nActuals - B"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["ℹ️ Input Collection\nActuals - A"];
  style 7 stroke:#2c3143,stroke-width:4px;
  8["Combine Matrices"];
  0 -->|output| 8;
  1 -->|output| 8;
  9["Get phenotype names"];
  8 -->|output| 9;
  10["Construct Expression Set Object"];
  8 -->|output| 10;
  9 -->|outfile| 10;
  11["MuSiC Deconvolution"];
  10 -->|out_rds| 11;
  5 -->|output| 11;
  3 -->|output| 11;
  4 -->|output| 11;
  2 -->|output| 11;
  5eeea4d0-88b4-49e2-99b0-66a2ea93119b["Output\nMuSiC Deconvolution on input dataset(s): Proportion Matrices"];
  11 --> 5eeea4d0-88b4-49e2-99b0-66a2ea93119b;
  style 5eeea4d0-88b4-49e2-99b0-66a2ea93119b stroke:#2c3143,stroke-width:4px;
  12["Transpose inferred cell proportions"];
  11 -->|props| 12;
  13["B_inferred"];
  12 -->|out_file| 13;
  14["A_inferred"];
  12 -->|out_file| 14;
  15["B_proportions_actual-infer"];
  13 -->|output| 15;
  6 -->|output| 15;
  16["A_proportions_actual-infer"];
  14 -->|output| 16;
  7 -->|output| 16;
  17["B - Music Results"];
  15 -->|outfile| 17;
  d495cd0f-623b-4f59-a4e9-94f498c75fa2["Output\nB - Music Results"];
  17 --> d495cd0f-623b-4f59-a4e9-94f498c75fa2;
  style d495cd0f-623b-4f59-a4e9-94f498c75fa2 stroke:#2c3143,stroke-width:4px;
  18["B - NNLS Results"];
  15 -->|outfile| 18;
  a81645e1-84b0-4b12-a608-722040f58e11["Output\nB - NNLS Results"];
  18 --> a81645e1-84b0-4b12-a608-722040f58e11;
  style a81645e1-84b0-4b12-a608-722040f58e11 stroke:#2c3143,stroke-width:4px;
  19["A - Music Results"];
  16 -->|outfile| 19;
  e9dc2c1e-1c9e-40cc-8288-d1a5bdf651fe["Output\nA - Music Results"];
  19 --> e9dc2c1e-1c9e-40cc-8288-d1a5bdf651fe;
  style e9dc2c1e-1c9e-40cc-8288-d1a5bdf651fe stroke:#2c3143,stroke-width:4px;
  20["A - NNLS Results"];
  16 -->|outfile| 20;
  9fcde9e0-cdcc-401b-8157-65340694268b["Output\nA - NNLS Results"];
  20 --> 9fcde9e0-cdcc-401b-8157-65340694268b;
  style 9fcde9e0-cdcc-401b-8157-65340694268b stroke:#2c3143,stroke-width:4px;

Inputs

Outputs

Tools

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/bulk-deconvolution-evaluate/workflows/deconv-eval-stage-2-deconv.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