Combined workflows for large genome assembly - upgraded

Run Workflow in Galaxy

• Galaxy France
• Galaxy Australia
• Galaxy Europe
• Galaxy Main
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nlong reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nR1"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nR2"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Parameter\nminimap settings for long reads"];
  style 3 fill:#ded,stroke:#393,stroke-width:4px;
  4["ℹ️ Input Dataset\nReference genome for Quast"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["🛠️ Subworkflow\nkmer counting - meryl - upgraded"];
  style 5 fill:#edd,stroke:#900,stroke-width:4px;
  1 -->|output| 5;
  6["🛠️ Subworkflow\nData QC - upgraded"];
  style 6 fill:#edd,stroke:#900,stroke-width:4px;
  1 -->|output| 6;
  2 -->|output| 6;
  0 -->|output| 6;
  7["🛠️ Subworkflow\nTrim and filter reads - fastp - upgraded "];
  style 7 fill:#edd,stroke:#900,stroke-width:4px;
  1 -->|output| 7;
  2 -->|output| 7;
  0 -->|output| 7;
  8["🛠️ Subworkflow\nAssembly with Flye - upgraded"];
  style 8 fill:#edd,stroke:#900,stroke-width:4px;
  7 -->|fastp filtered long reads| 8;
  9["🛠️ Subworkflow\nAssembly polishing - upgraded"];
  style 9 fill:#edd,stroke:#900,stroke-width:4px;
  8 -->|Flye assembly on input datasets consensus| 9;
  7 -->|fastp filtered R1 reads| 9;
  7 -->|fastp filtered long reads| 9;
  3 -->|output| 9;
  10["🛠️ Subworkflow\nAssess genome quality - upgraded"];
  style 10 fill:#edd,stroke:#900,stroke-width:4px;
  9 -->|Assembly polished by long reads using Medaka| 10;
  4 -->|output| 10;

Inputs

Outputs

Tools

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

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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.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