Combined workflows for large genome assembly - upgraded
assembly-largegenome/galaxy-workflow-combined-workflows-for-large-genome-assembly
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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
Input | Label |
---|---|
Input dataset | long reads |
Input dataset | R1 |
Input dataset | R2 |
Input parameter | minimap settings (for long reads) |
Input dataset | Reference genome for Quast |
Outputs
From | Output | Label |
---|---|---|
Input parameter | minimap settings (for long reads) | |
Assembly polishing - upgraded |
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
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-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:
Video: Importing a workflow from URL
Version History
Version | Commit | Time | Comments |
---|---|---|---|
5 | 01cffeed0 | 2024-05-07 09:32:46 | Update Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.ga |
4 | e8ddbcdd5 | 2024-05-01 04:32:16 | new versions of workflows |
3 | bd0db2c96 | 2024-05-01 04:21:14 | Rename Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.ga to Galaxy-Workflow-Combined_workflows_for_large_genome_assembly_old.ga |
2 | 62e77944b | 2023-02-17 09:53:23 | add/complete creator info on workflows |
1 | 9fcb3aeec | 2022-10-07 06:24:16 | large genome tutorial |
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