MuSiC Workflow

single-cell-bulk-music/main-workflow

Author(s)

Version
2
Last updated
May 15, 2023
License
None Specified, defaults to CC-BY-4.0
Tags
transcriptomics
single-cell

Features
Tutorial
Bulk RNA Deconvolution with MuSiC
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00186
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nscRNA Assay Tabular"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nscRNA Phenotype Tabular"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Parameter\nscRNA Metadata"];
  style 2 fill:#ded,stroke:#393,stroke-width:4px;
  3["ℹ️ Input Dataset\nBulk RNA Assay Tabular"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Parameter\nBulk RNA Annotation"];
  style 4 fill:#ded,stroke:#393,stroke-width:4px;
  5["ℹ️ Input Parameter\nCell Types List"];
  style 5 fill:#ded,stroke:#393,stroke-width:4px;
  6["ℹ️ Input Dataset\nCell Markers C1"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["ℹ️ Input Dataset\nCell Markers C2"];
  style 7 stroke:#2c3143,stroke-width:4px;
  8["Construct scRNA ESet Object"];
  0 -->|output| 8;
  2 -->|output| 8;
  1 -->|output| 8;
  872b3dd2-322c-47cc-b5b9-071a9f939320["Output\nConstruct Expression Set Object on input dataset(s): RData ESet Object"];
  8 --> 872b3dd2-322c-47cc-b5b9-071a9f939320;
  style 872b3dd2-322c-47cc-b5b9-071a9f939320 stroke:#2c3143,stroke-width:4px;
  9["Construct Bulk RNA ESet Object"];
  4 -->|output| 9;
  3 -->|output| 9;
  10["Extract Cell Types"];
  8 -->|out_rds| 10;
  11["Extract General Info"];
  8 -->|out_rds| 11;
  1733593f-847d-4adb-91f4-fd78c077b074["Output\nInspect Expression Set Object on input dataset(s): Inspection Result"];
  11 --> 1733593f-847d-4adb-91f4-fd78c077b074;
  style 1733593f-847d-4adb-91f4-fd78c077b074 stroke:#2c3143,stroke-width:4px;
  12["Extract General Info Bulk"];
  9 -->|out_rds| 12;
  13["Music: Estimate Cell Proportions"];
  9 -->|out_rds| 13;
  5 -->|output| 13;
  8 -->|out_rds| 13;
  14["Music: Compute Dendrogram"];
  9 -->|out_rds| 14;
  6 -->|output| 14;
  7 -->|output| 14;
  8 -->|out_rds| 14;
  df2e83a5-ac67-460f-8b0f-ac3f3b63280f["Output\nMuSiC on input dataset(s): PDF Plots"];
  14 --> df2e83a5-ac67-460f-8b0f-ac3f3b63280f;
  style df2e83a5-ac67-460f-8b0f-ac3f3b63280f stroke:#2c3143,stroke-width:4px;

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 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:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
2 e2453dfb5 2023-05-15 14:00:47 use full tool ID
1 327fd2b84 2022-11-12 17:14:25 Making a single cell topics

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music/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