flowchart TD
0["ℹ️ Input Dataset\nAssembly to be polished"];
style 0 stroke:#2c3143,stroke-width:4px;
1["ℹ️ Input Dataset\nlong reads"];
style 1 stroke:#2c3143,stroke-width:4px;
2["ℹ️ Input Parameter\nminimap setting for long reads"];
style 2 fill:#ded,stroke:#393,stroke-width:4px;
3["ℹ️ Input Dataset\nIllumina reads R1"];
style 3 stroke:#2c3143,stroke-width:4px;
4["🛠️ Subworkflow\nRacon polish with long reads, x4 - upgraded"];
style 4 fill:#edd,stroke:#900,stroke-width:4px;
0 -->|output| 4;
1 -->|output| 4;
2 -->|output| 4;
5["Medaka polish"];
4 -->|Assembly polished by long reads using Racon| 5;
1 -->|output| 5;
e3136060-bce7-4af3-87c4-9dcbb0d1f531["Output\nAssembly polished by long reads using Medaka"];
5 --> e3136060-bce7-4af3-87c4-9dcbb0d1f531;
style e3136060-bce7-4af3-87c4-9dcbb0d1f531 stroke:#2c3143,stroke-width:4px;
6["Fasta statistics after Racon long read polish"];
4 -->|Assembly polished by long reads using Racon| 6;
7["Fasta statistics after Medaka polish"];
5 -->|out_consensus| 7;
8["🛠️ Subworkflow\nRacon polish with Illumina reads R1 only, x2 - upgraded"];
style 8 fill:#edd,stroke:#900,stroke-width:4px;
5 -->|out_consensus| 8;
3 -->|output| 8;
9["Fasta statistics after Racon short read polish"];
8 -->|Assembly polished by short reads using Racon| 9;
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 galaxy-uploadImport 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:
Download Workflow RO-Crate
View on WorkflowHub