Workflows

These workflows are associated with Pre-processing of Single-Cell RNA Data

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.

flowchart TD
  0["ℹ️ Input Collection\nList of FACS pairs"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nBarcodes"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nGTF file UCSC"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Flatten Collection"];
  0 -->|output| 3;
  4["🛠️ Subworkflow\nCelSeq2: Single Batch mm10"];
  style 4 fill:#edd,stroke:#900,stroke-width:4px;
  1 -->|output| 4;
  3 -->|output| 4;
  2 -->|output| 4;
  5["Column Join"];
  4 -->|9:out_counts| 5;
	

flowchart TD
  0["ℹ️ Input Collection\nBatch"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nBarcodes single-col"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nGTF file UCSC"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["UMI-tools extract"];
  1 -->|output| 3;
  0 -->|output| 3;
  4["Alignment Choose a Genome"];
  2 -->|output| 4;
  3 -->|out2| 4;
  5["Filter"];
  4 -->|mapped_reads| 5;
  6["featureCounts"];
  5 -->|out_file1| 6;
  2 -->|output| 6;
  7["UMI-tools count"];
  6 -->|output_bam| 7;
	

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: