Metagenomics assembly tutorial workflow

microbiome-metagenomics-assembly/metagenomics-assembly-tutorial-workflow

Author(s)

Version
1
Last updated
Jan 11, 2024
License
None Specified, defaults to CC-BY-4.0
Tags

Features
Tutorial
Assembly of metagenomic sequencing data
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00125
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Collection\nInput Dataset Collection"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["metaSPAdes"];
  0 -->|output| 1;
  833d79ff-e16f-414c-9c41-db8dbfa8ed6b["Output\nmetaSPAdes on input dataset(s): Scaffolds"];
  1 --> 833d79ff-e16f-414c-9c41-db8dbfa8ed6b;
  style 833d79ff-e16f-414c-9c41-db8dbfa8ed6b stroke:#2c3143,stroke-width:4px;
  10319152-d2f9-47d8-be41-f956a57e86d3["Output\nmetaSPAdes on input dataset(s): Assembly graph"];
  1 --> 10319152-d2f9-47d8-be41-f956a57e86d3;
  style 10319152-d2f9-47d8-be41-f956a57e86d3 stroke:#2c3143,stroke-width:4px;
  b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633["Output\nmetaSPAdes on input dataset(s): Assembly graph with scaffolds"];
  1 --> b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633;
  style b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633 stroke:#2c3143,stroke-width:4px;
  b6b74c9d-5a16-4725-a1d1-11c1f05ee909["Output\nmetaSPAdes on input dataset(s): Contigs"];
  1 --> b6b74c9d-5a16-4725-a1d1-11c1f05ee909;
  style b6b74c9d-5a16-4725-a1d1-11c1f05ee909 stroke:#2c3143,stroke-width:4px;
  2["MEGAHIT"];
  0 -->|output| 2;
  3["Bowtie2"];
  0 -->|output| 3;
  2 -->|output| 3;
  4["megahit contig2fastg"];
  2 -->|output| 4;
  5["Quast"];
  2 -->|output| 5;
  0 -->|output| 5;
  6["Bandage Image"];
  4 -->|fastg| 6;
  7["Bandage Info"];
  4 -->|fastg| 7;
  8["Column join"];
  7 -->|outfile| 8;

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 0e0a2f2cc 2024-01-10 15:47:09 Rename metagenomics topic to microbiome

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metagenomics-assembly/workflows/metagenomics_assembly_tutorial_workflow.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