Understanding Barcodes

single-cell-scrna-umis/understanding-barcodes

Author(s)
Morgan
Version
1
Last updated
Feb 13, 2025
License
MIT
Tags
name:single-cell

Features
Tutorial
Understanding Barcodes
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00314
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 Collection\nFastQ data"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nReads filter list"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["FastQC"];
  0 -->|output| 2;
  2908b4d8-2981-460a-af3a-6bc63b333e77["Output\ntext_file"];
  2 --> 2908b4d8-2981-460a-af3a-6bc63b333e77;
  style 2908b4d8-2981-460a-af3a-6bc63b333e77 stroke:#2c3143,stroke-width:4px;
  3f629c3a-7de6-416a-82a5-5dd7363c42da["Output\nhtml_file"];
  2 --> 3f629c3a-7de6-416a-82a5-5dd7363c42da;
  style 3f629c3a-7de6-416a-82a5-5dd7363c42da stroke:#2c3143,stroke-width:4px;
  3["Filter sequences by ID"];
  1 -->|output| 3;
  0 -->|output| 3;
  1422ca8b-1aed-418d-9821-d5afff9ac4b5["Output\noutput_pos"];
  3 --> 1422ca8b-1aed-418d-9821-d5afff9ac4b5;
  style 1422ca8b-1aed-418d-9821-d5afff9ac4b5 stroke:#2c3143,stroke-width:4px;
  4["UMI-tools extract"];
  3 -->|output_pos| 4;
  d762b062-8f10-4f60-8826-0a325ec6f4b8["Output\nout_paired_collection"];
  4 --> d762b062-8f10-4f60-8826-0a325ec6f4b8;
  style d762b062-8f10-4f60-8826-0a325ec6f4b8 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset collection FastQ data
Input dataset Reads filter list

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 FastQC
toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.9 Filter sequences by ID
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.6+galaxy0 UMI-tools extract

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.6+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.9 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
1 22a35bdb2 2025-02-12 16:57:20 add tutorial workflow

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-umis/workflows/Understanding-Barcodes.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