Unicycler training

assembly-unicycler-assembly/unicycler

Author(s)

Version
4
Last updated
Mar 15, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
assembly

Features
Tutorial
Unicycler Assembly
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00020
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\nForward reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nReverse Reads"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nLong Reads"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["FastQC"];
  0 -->|output| 3;
  4["FastQC"];
  1 -->|output| 4;
  5["Create assemblies with Unicycler"];
  2 -->|output| 5;
  0 -->|output| 5;
  1 -->|output| 5;
  6["MultiQC"];
  3 -->|text_file| 6;
  4 -->|text_file| 6;
  7["Quast"];
  5 -->|assembly| 7;
  8["Prokka"];
  5 -->|assembly| 8;
  0d6b33c9-b105-4997-9045-b86e52f00156["Output\ntbl"];
  8 --> 0d6b33c9-b105-4997-9045-b86e52f00156;
  style 0d6b33c9-b105-4997-9045-b86e52f00156 stroke:#2c3143,stroke-width:4px;
  8e08b54d-87e1-4269-9b96-8ebf1a9bb4ab["Output\ngbk"];
  8 --> 8e08b54d-87e1-4269-9b96-8ebf1a9bb4ab;
  style 8e08b54d-87e1-4269-9b96-8ebf1a9bb4ab stroke:#2c3143,stroke-width:4px;
  65e4ddf9-f5bc-4078-8b4e-37b332e12ece["Output\nffn"];
  8 --> 65e4ddf9-f5bc-4078-8b4e-37b332e12ece;
  style 65e4ddf9-f5bc-4078-8b4e-37b332e12ece stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Forward reads
Input dataset Reverse Reads
Input dataset Long Reads

Outputs

From Output Label
Input dataset Forward reads
Input dataset Reverse Reads
Input dataset Long Reads
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 FastQC
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 FastQC
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0 Create assemblies with Unicycler
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 MultiQC
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy0 Quast
toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5 Prokka

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0 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
9 232ce0372 2020-02-13 17:30:57 removed name label bit
8 cccd85216 2020-02-13 17:13:18 minor tweaks and files unhidden
7 2a2b6329e 2020-02-07 17:15:35 name fixed
6 3d424d5e6 2020-02-06 18:40:37 annotation fixed
5 2eade3cbf 2020-02-06 16:00:07 tags added
4 076420647 2020-01-27 14:26:47 workflows updated with newer tools, added missing
3 667ff3de9 2020-01-22 10:59:29 annotation
2 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
1 02b1037e8 2018-05-22 16:04:33 add testing for unicycler

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/assembly/tutorials/unicycler-assembly/workflows/unicycler.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