Workflows

These workflows are associated with Single-cell quality control with scater

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.

Scater

Last updated Nov 12, 2022

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Tests: ❌ Results: Not yet automated

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["Scater: plot library QC"];
  3 -->|output_loom| 4;
  5["Scater: filter SCE"];
  3 -->|output_loom| 5;
  6["Scater: plot library QC"];
  5 -->|output_loom| 6;
  7["Scater: PCA plot"];
  5 -->|output_loom| 7;
	

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