Workflows

These workflows are associated with Pre-processing of 10X Single-Cell RNA Datasets

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.

Preprocessing of 10X scRNA-seq data
Wendi Bacon, Pavankumar Videm, Mehmet Tekman, Hans-Rudolf Hotz, Daniel Blankenberg

Last updated May 18, 2023

Launch in Tutorial Mode
License: CC-BY-4.0
Tests: ✅ Results: Not yet automated

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flowchart TD
  0["ℹ️ Input Dataset\nHomo_sapiens.GRCh37.75.gtf"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nsubset_pbmc_1k_v3_S1_L001_R1_001.fastq.gz"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nsubset_pbmc_1k_v3_S1_L002_R1_001.fastq.gz"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nsubset_pbmc_1k_v3_S1_L002_R2_001.fastq.gz"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nsubset_pbmc_1k_v3_S1_L001_R2_001.fastq.gz"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\n3M-february-2018.txt.gz"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["RNA STARSolo"];
  0 -->|output| 6;
  1 -->|output| 6;
  2 -->|output| 6;
  3 -->|output| 6;
  4 -->|output| 6;
  5 -->|output| 6;
  7["DropletUtils"];
  6 -->|output_matrix| 7;
  6 -->|output_barcodes| 7;
  6 -->|output_genes| 7;
  8["DropletUtils"];
  6 -->|output_matrix| 8;
  6 -->|output_barcodes| 8;
  6 -->|output_genes| 8;
  9["DropletUtils"];
  6 -->|output_matrix| 9;
  6 -->|output_barcodes| 9;
  6 -->|output_genes| 9;

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: