Workflows
These workflows are associated with Calling very rare variants
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.
Du Novo GTN Tutorial - Make Consensus Sequences
Last updated Jan 17, 2020
Launch in Tutorial Mode
License:
None Specified, defaults to
CC-BY-4.0
Tests: ❌
Results: Not yet automated
flowchart TD 0["ℹ️ Input Dataset\nSRR1799908_forward"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nSRR1799908_reverse"]; style 1 stroke:#2c3143,stroke-width:4px; 2["Du Novo: Make families"]; 0 -->|output| 2; 1 -->|output| 2; 3["Du Novo: Correct barcodes"]; 2 -->|output| 3; 4["Du Novo: Align families"]; 3 -->|output| 4; 5["Du Novo: Make consensus reads"]; 4 -->|output| 5; 6["DCS: Sequence Content Trimmer"]; 5 -->|dcs1| 6; 5 -->|dcs2| 6; 7["SSCS: Sequence Content Trimmer"]; 5 -->|sscs1| 7; 5 -->|sscs2| 7; 75dfe52d-711e-4826-ba9b-b4feed30f5bf["Output\n"]; 7 --> 75dfe52d-711e-4826-ba9b-b4feed30f5bf; style 75dfe52d-711e-4826-ba9b-b4feed30f5bf stroke:#2c3143,stroke-width:4px;
Du Novo GTN Tutorial - Variant Calling
Last updated Jan 17, 2020
Launch in Tutorial Mode
License:
None Specified, defaults to
CC-BY-4.0
Tests: ❌
Results: Not yet automated
flowchart TD 0["ℹ️ Input Dataset\nTrimmed reads mate 1"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nTrimmed reads mate 2"]; style 1 stroke:#2c3143,stroke-width:4px; 2["Map with BWA-MEM"]; 0 -->|output| 2; 1 -->|output| 2; 3["BamLeftAlign"]; 2 -->|bam_output| 3; 4["Naive Variant Caller NVC"]; 3 -->|output_bam| 4; 5["Variant Annotator"]; 4 -->|output_vcf| 5; 6["Filter"]; 5 -->|output| 6;
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