Single-cell QC with scater

single-cell-scrna-scater-qc/main-workflow

Author(s)
Graham Etherington, Nicola Soranzo, Pavankumar Videm
Version
2
Last updated
Jan 14, 2025
License
CC-BY-4.0
Tags
transcriptomics
single-cell

Features
Tutorial
Single-cell quality control with scater
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00213
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nannotation.txt"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\ncounts.txt"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nmt_controls.txt"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Scater: Calculate QC metrics"];
  0 -->|output| 3;
  1 -->|output| 3;
  2 -->|output| 3;
  4["Library QC"];
  3 -->|output_loom| 4;
  57113c0a-f622-42df-8a5b-5bc4329d64d4["Output\nlib_qc_plot"];
  4 --> 57113c0a-f622-42df-8a5b-5bc4329d64d4;
  style 57113c0a-f622-42df-8a5b-5bc4329d64d4 stroke:#2c3143,stroke-width:4px;
  5["Filter SCE"];
  3 -->|output_loom| 5;
  6d503142-e29b-4c13-9773-c8176419dfb6["Output\noutput_loom"];
  5 --> 6d503142-e29b-4c13-9773-c8176419dfb6;
  style 6d503142-e29b-4c13-9773-c8176419dfb6 stroke:#2c3143,stroke-width:4px;
  6["Filtered Library QC"];
  5 -->|output_loom| 6;
  f7783f97-b108-4850-ac08-fc7d0769e8d8["Output\nfiltered_lib_qc_plot"];
  6 --> f7783f97-b108-4850-ac08-fc7d0769e8d8;
  style f7783f97-b108-4850-ac08-fc7d0769e8d8 stroke:#2c3143,stroke-width:4px;
  7["PCA Plot"];
  5 -->|output_loom| 7;
  4ca6aec7-1024-4988-b975-428cfa7603ed["Output\npca_plot"];
  7 --> 4ca6aec7-1024-4988-b975-428cfa7603ed;
  style 4ca6aec7-1024-4988-b975-428cfa7603ed stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset annotation.txt
Input dataset counts.txt
Input dataset mt_controls.txt

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.12.2 Scater: plot library QC Library QC
toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.12.2 Scater: filter SCE Filter SCE
toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.12.2 Scater: plot library QC Filtered Library QC
toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/1.12.2 Scater: PCA plot PCA Plot

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.12.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.12.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.12.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/1.12.2 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 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
3 a8f264c33 2025-01-14 14:17:42 rename WF
2 0382ac8b8 2024-12-12 18:24:06 Add workflow tests for Scater QC workflow
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/scrna-scater-qc/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