MuSiC Workflow

single-cell-bulk-music/main-workflow

Author(s)

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

Features

Tutorial
hands_on Bulk RNA Deconvolution with MuSiC

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl 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 question
galaxy-download 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;

Inputs

Input Label
Input dataset scRNA Assay Tabular
Input dataset scRNA Phenotype Tabular
Input parameter scRNA Metadata
Input dataset Bulk RNA Assay Tabular
Input parameter Bulk RNA Annotation
Input parameter Cell Types List
Input dataset Cell Markers C1
Input dataset Cell Markers C2

Outputs

From Output Label
Input dataset scRNA Assay Tabular
Input dataset scRNA Phenotype Tabular
Input parameter scRNA Metadata
Input dataset Bulk RNA Assay Tabular
Input parameter Bulk RNA Annotation
Input parameter Cell Types List
Input dataset Cell Markers C1
Input dataset Cell Markers C2
toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0 Construct Expression Set Object Construct scRNA ESet Object
toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0 Construct Expression Set Object Construct Bulk RNA ESet Object
toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3 Inspect Expression Set Object Extract Cell Types
toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3 Inspect Expression Set Object Extract General Info
toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3 Inspect Expression Set Object Extract General Info (Bulk)
toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy3 MuSiC Music: Estimate Cell Proportions
toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy3 MuSiC Music: Compute Dendrogram

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3 View in ToolShed

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-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:

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