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.

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;
	

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

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: